Upd subsample

CHANGELOG.md

@@ -39,6 +39,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#286](https://github.com/nf-core/phaseimpute/pull/286) - Remove unecessary `saveAs` from config thanks to topic migration.
 - [#291](https://github.com/nf-core/phaseimpute/pull/291) - Update TEMPLATE to nf-core tools version 4.0.2.
 - [#292](https://github.com/nf-core/phaseimpute/pull/292) - Reorganise and rename pipeline level tests.
+- [#296](https://github.com/nf-core/phaseimpute/pull/296) - Replace `SAMTOOLS_DEPTH` by `SAMTOOLS_COVERAGE` in downsampling subworkflow to reduce computational load and allow region specificity.
 
 ### `Fixed`
 

conf/steps/simulation.config

@@ -46,16 +46,10 @@ process {
         ]
     }
 
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_SUBSAMPLEDEPTH_SAMTOOLS:SAMTOOLS_DEPTH' {
-        ext.prefix = { "${meta1.id}_C${meta1.chr ?: "all"}.depth" }
-        tag = {"${meta1.id} ${meta1.chr ?: "all"}"}
-    }
-
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_SUBSAMPLEDEPTH_SAMTOOLS:GAWK' {
-        ext.args2 = "'{ total += \$3 } END { print total/NR }'"
-        ext.prefix = { "${meta.id}_C${meta.chr ?: "all"}.depth.mean" }
-        ext.suffix = "tsv"
-        tag = {"${meta.id} ${meta.chr ?: "all"}"}
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_SUBSAMPLEDEPTH_SAMTOOLS:SAMTOOLS_COVERAGE' {
+        ext.args = { meta.region ? "--region ${meta.region}" : "" }
+        ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.depth" }
+        tag = {"${meta.id} ${meta.region}"}
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_SUBSAMPLEDEPTH_SAMTOOLS:SAMTOOLS_VIEW' {

docs/usage.md

@@ -423,6 +423,10 @@ The required flags for this mode are:
 - `--depth`: The final depth of the file [default: 1].
 - `--genome` or `--fasta`: The reference genome of the samples.
 
+If your input files encompass only a portion of chromosomes, please provide the exact regions in the [regions samplesheet](#samplesheet-region).
+If not provided, the input data coverage estimation will be underestimate and will either result in an error or in erroneous
+resulting depth.
+
 You can find an overview of the results produced by this step in the [Output](output.md).
 
 ## Start with panel preparation `--steps panelprep`

modules.json

@@ -168,8 +168,8 @@
                     },
                     "samtools/coverage": {
                         "branch": "master",
-                        "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205",
-                        "installed_by": ["modules"]
+                        "git_sha": "54d9a8659816764fc144e6f7fba1679f57328153",
+                        "installed_by": ["bam_subsampledepth_samtools"]
                     },
                     "samtools/depth": {
                         "branch": "master",
@@ -198,8 +198,8 @@
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "2057a0a8dbd67000d08613a556570aa7184a7c89",
-                        "installed_by": ["bam_subsampledepth_samtools", "modules"]
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "installed_by": ["bam_subsampledepth_samtools"]
                     },
                     "shapeit5/ligate": {
                         "branch": "master",
@@ -252,7 +252,7 @@
                     },
                     "bam_subsampledepth_samtools": {
                         "branch": "master",
-                        "git_sha": "2057a0a8dbd67000d08613a556570aa7184a7c89",
+                        "git_sha": "54d9a8659816764fc144e6f7fba1679f57328153",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_variant_calling_mpileup_bcftools": {