Move seqeralabs/action-tower-launch to @v2 (v2.4.0)

[mashehu]

This moves seqeralabs/action-tower-launch to the @v2 tag, which now points to v2.4.0, in the AWS test workflows.

Earlier versions only scrubbed the Seqera Platform access token from the uploaded tower_action_*.log debug artifact when the launch succeeded. v2.4.0 always removes it. It also stops running tw launch in verbose mode by default (from v2.3.0) and adds a link to the launched run to the job summary.

The next template sync makes the same change on dev.

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e0ddbdd

+| ✅ 277 tests passed       |+
#| ❔   3 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  15 tests had warnings |!

Details

❗ Test warnings:

• pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
• pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
• pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
• pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
• pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
• schema_description - No description provided in schema for parameter: igenomes_base
• schema_description - No description provided in schema for parameter: igenomes_ignore
• schema_description - No description provided in schema for parameter: tracedir
• schema_description - No description provided in schema for parameter: hostnames
• schema_description - No description provided in schema for parameter: version
• schema_description - No description provided in schema for parameter: hook_url
• schema_description - No description provided in schema for parameter: pipelines_testdata_base_path
• schema_description - No description provided in schema for parameter: validate_params
• schema_description - No description provided in schema for parameter: config_profile_name
• included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ Tests ignored:

• files_exist - File is ignored: .github/workflows/linting_comment.yml
• files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

❔ Tests fixed:

• rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .gitignore
• files_exist - File found: .nf-core.yml
• files_exist - File found: .prettierignore
• files_exist - File found: .prettierrc.yml
• files_exist - File found: CHANGELOG.md
• files_exist - File found: CITATIONS.md
• files_exist - File found: CODE_OF_CONDUCT.md
• files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_exist - File found: nextflow_schema.json
• files_exist - File found: nextflow.config
• files_exist - File found: README.md
• files_exist - File found: .github/.dockstore.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
• files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
• files_exist - File found: .github/workflows/branch.yml
• files_exist - File found: .github/workflows/nf-test.yml
• files_exist - File found: .github/actions/get-shards/action.yml
• files_exist - File found: .github/actions/nf-test/action.yml
• files_exist - File found: .github/workflows/pr-comment.yml
• files_exist - File found: .github/workflows/linting.yml
• files_exist - File found: assets/email_template.html
• files_exist - File found: assets/email_template.txt
• files_exist - File found: assets/sendmail_template.txt
• files_exist - File found: assets/nf-core-tumourevo_logo_light.png
• files_exist - File found: conf/modules.config
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• files_exist - File found: docs/CONTRIBUTING.md
• files_exist - File found: docs/images/nf-core-tumourevo_logo_light.png
• files_exist - File found: docs/images/nf-core-tumourevo_logo_dark.png
• files_exist - File found: docs/output.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/usage.md
• files_exist - File found: nf-test.config
• files_exist - File found: tests/default.nf.test
• files_exist - File found: main.nf
• files_exist - File found: assets/multiqc_config.yml
• files_exist - File found: conf/base.config
• files_exist - File found: conf/igenomes.config
• files_exist - File found: conf/igenomes_ignored.config
• files_exist - File found: .github/workflows/awstest.yml
• files_exist - File found: .github/workflows/awsfulltest.yml
• files_exist - File found: modules.json
• files_exist - File found: ro-crate-metadata.json
• files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
• files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
• files_exist - File not found check: .github/workflows/push_dockerhub.yml
• files_exist - File not found check: .markdownlint.yml
• files_exist - File not found check: .nf-core.yaml
• files_exist - File not found check: .yamllint.yml
• files_exist - File not found check: bin/markdown_to_html.r
• files_exist - File not found check: conf/aws.config
• files_exist - File not found check: docs/images/nf-core-tumourevo_logo.png
• files_exist - File not found check: lib/Checks.groovy
• files_exist - File not found check: lib/Completion.groovy
• files_exist - File not found check: lib/NfcoreTemplate.groovy
• files_exist - File not found check: lib/Utils.groovy
• files_exist - File not found check: lib/Workflow.groovy
• files_exist - File not found check: lib/WorkflowMain.groovy
• files_exist - File not found check: lib/WorkflowTumourevo.groovy
• files_exist - File not found check: parameters.settings.json
• files_exist - File not found check: pipeline_template.yml
• files_exist - File not found check: Singularity
• files_exist - File not found check: lib/nfcore_external_java_deps.jar
• files_exist - File not found check: .travis.yml
• nextflow_config - Found nf-schema plugin
• nextflow_config - Config variable found: manifest.name
• nextflow_config - Config variable found: manifest.nextflowVersion
• nextflow_config - Config variable found: manifest.description
• nextflow_config - Config variable found: manifest.version
• nextflow_config - Config variable found: manifest.homePage
• nextflow_config - Config variable found: timeline.enabled
• nextflow_config - Config variable found: trace.enabled
• nextflow_config - Config variable found: report.enabled
• nextflow_config - Config variable found: dag.enabled
• nextflow_config - Config variable found: process.cpus
• nextflow_config - Config variable found: process.memory
• nextflow_config - Config variable found: process.time
• nextflow_config - Config variable found: params.outdir
• nextflow_config - Config variable found: params.input
• nextflow_config - Config variable found: manifest.mainScript
• nextflow_config - Config variable found: timeline.file
• nextflow_config - Config variable found: trace.file
• nextflow_config - Config variable found: report.file
• nextflow_config - Config variable found: dag.file
• nextflow_config - Config variable (correctly) not found: params.nf_required_version
• nextflow_config - Config variable (correctly) not found: params.container
• nextflow_config - Config variable (correctly) not found: params.singleEnd
• nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
• nextflow_config - Config variable (correctly) not found: params.name
• nextflow_config - Config variable (correctly) not found: params.enable_conda
• nextflow_config - Config variable (correctly) not found: params.max_cpus
• nextflow_config - Config variable (correctly) not found: params.max_memory
• nextflow_config - Config variable (correctly) not found: params.max_time
• nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
• nextflow_config - Config variable (correctly) not found: params.validationLenientMode
• nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
• nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
• nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
• nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
• nextflow_config - Config timeline.enabled had correct value: True
• nextflow_config - Config report.enabled had correct value: True
• nextflow_config - Config trace.enabled had correct value: True
• nextflow_config - Config dag.enabled had correct value: True
• nextflow_config - Config manifest.name began with nf-core/
• nextflow_config - Config manifest.homePage began with https://github.com/nf-core/
• nextflow_config - Config dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config manifest.version does not contain dev for release: 1.0.0
• nextflow_config - Config params.custom_config_version is set to master
• nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Lines for loading custom profiles found
• nextflow_config - nextflow.config contains configuration profile test
• nextflow_config - Config default value correct: params.genome= GRCh38
• nextflow_config - Config default value correct: params.tools= tinc,mobster,viber,pyclone-vi,sparsesignatures,sigprofiler
• nextflow_config - Config default value correct: params.publish_dir_mode= copy
• nextflow_config - Config default value correct: params.download_cache_vep= true
• nextflow_config - Config default value correct: params.vep_custom_args= --everything --filter_common --per_gene --total_length --offline --format vcf
• nextflow_config - Config default value correct: params.drivers_table= https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/tumourevo/data/DRIVER_ANNOTATION/ANNOTATE_DRIVER/Compendium_Cancer_Genes.tsv
• nextflow_config - Config default value correct: params.vcf_filter_mutations= true
• nextflow_config - Config default value correct: params.cnaqc_min_absolute_karyotype_mutations= 100
• nextflow_config - Config default value correct: params.cnaqc_purity_error= 0.05
• nextflow_config - Config default value correct: params.cnaqc_matching_strategy= rightmost
• nextflow_config - Config default value correct: params.cnaqc_muts_per_karyotype= 25
• nextflow_config - Config default value correct: params.cnaqc_blacklist_indels= TRUE
• nextflow_config - Config default value correct: params.joincnaqc_keep_original= TRUE
• nextflow_config - Config default value correct: params.pyclonevi_density= beta-binomial
• nextflow_config - Config default value correct: params.pyclonevi_n_restarts= 100
• nextflow_config - Config default value correct: params.pyclonevi_n_grid_point= 100
• nextflow_config - Config default value correct: params.pyclonevi_n_cluster= 20
• nextflow_config - Config default value correct: params.mobster_tail= TRUE
• nextflow_config - Config default value correct: params.mobster_pi_cutoff= 0.02
• nextflow_config - Config default value correct: params.mobster_k= 1:5
• nextflow_config - Config default value correct: params.mobster_min_vaf= 0.05
• nextflow_config - Config default value correct: params.mobster_n_cutoff= 10
• nextflow_config - Config default value correct: params.viber_k= 10
• nextflow_config - Config default value correct: params.viber_binomial_cutoff= 0.05
• nextflow_config - Config default value correct: params.viber_pi_cutoff= 0.02
• nextflow_config - Config default value correct: params.viber_re_assign= FALSE
• nextflow_config - Config default value correct: params.viber_dimensions_cutoff= 1
• nextflow_config - Config default value correct: params.sparsesignatures_iterations= 30
• nextflow_config - Config default value correct: params.sparsesignatures_k= 3:10
• nextflow_config - Config default value correct: params.sparsesignatures_nmf_runs= 10
• nextflow_config - Config default value correct: params.sparsesignatures_max_iterations_lasso= 10000
• nextflow_config - Config default value correct: params.sparsesignatures_num_processes= all
• nextflow_config - Config default value correct: params.sparsesignatures_cross_validation_entries= 0.01
• nextflow_config - Config default value correct: params.sparsesignatures_cross_validation_repetitions= 50
• nextflow_config - Config default value correct: params.sparsesignatures_cross_validation_iterations= 5
• nextflow_config - Config default value correct: params.sparsesignatures_lambda_values_beta= c(0.01, 0.05, 0.1, 0.2)
• nextflow_config - Config default value correct: params.sparsesignatures_lambda_rate_alpha= 0
• nextflow_config - Config default value correct: params.sparsesignatures_seed= 42
• nextflow_config - Config default value correct: params.sparsesignatures_lambda_values_alpha= c(0.00, 0.01, 0.05, 0.10)
• nextflow_config - Config default value correct: params.publish_dir_mode_genome_sigprofiler= move
• nextflow_config - Config default value correct: params.download_sigprofiler_genome= true
• nextflow_config - Config default value correct: params.sigprofiler_input_type= matrix
• nextflow_config - Config default value correct: params.sigprofiler_minimum_signatures= 1
• nextflow_config - Config default value correct: params.sigprofiler_maximum_signatures= 25
• nextflow_config - Config default value correct: params.sigprofiler_context_type= 96,DINUC,ID
• nextflow_config - Config default value correct: params.sigprofiler_nmf_replicates= 100
• nextflow_config - Config default value correct: params.sigprofiler_min_nmf_iterations= 10000
• nextflow_config - Config default value correct: params.sigprofiler_max_nmf_iterations= 1000000
• nextflow_config - Config default value correct: params.sigprofiler_nmf_test_conv= 10000
• nextflow_config - Config default value correct: params.tinc_normal_contamination_lv= 3
• nextflow_config - Config default value correct: params.custom_config_version= master
• nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
• nextflow_config - Config default value correct: params.tracedir= null/pipeline_info
• nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
• nextflow_config - Config default value correct: params.validate_params= true
• nf_test_content - 'tests/stub.nf.test' contains outdir parameter
• nf_test_content - 'tests/stub.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/stub.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/default.nf.test' contains outdir parameter
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
• nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
• nf_test_content - 'nf-test.config' sets a testsDir
• nf_test_content - 'nf-test.config' sets a workDir
• nf_test_content - 'nf-test.config' sets a configFile
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - CODE_OF_CONDUCT.md matches the template
• files_unchanged - LICENSE matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
• files_unchanged - .github/workflows/pr-comment.yml matches the template
• files_unchanged - assets/email_template.html matches the template
• files_unchanged - assets/email_template.txt matches the template
• files_unchanged - assets/sendmail_template.txt matches the template
• files_unchanged - assets/nf-core-tumourevo_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-tumourevo_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-tumourevo_logo_dark.png matches the template
• files_unchanged - docs/README.md matches the template
• files_unchanged - .gitignore matches the template
• files_unchanged - .prettierignore matches the template
• actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
• actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
• actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
• actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
• actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
• readme - README Nextflow minimum version badge matched config. Badge: 25.10.4, Config: 25.10.4
• readme - README nf-core template version badge found.
• readme - README Zenodo placeholder was replaced with DOI.
• pipeline_if_empty_null - No ifEmpty(null) strings found
• plugin_includes - No wrong validation plugin imports have been found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (0 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: pr-comment.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• multiqc_config - assets/multiqc_config.yml found and not ignored.
• multiqc_config - assets/multiqc_config.yml contains report_section_order
• multiqc_config - assets/multiqc_config.yml contains export_plots
• multiqc_config - assets/multiqc_config.yml contains report_comment
• multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
• multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
• multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• modules_config - conf/modules.config found and not ignored.
• modules_config - BCFTOOLS_VIEW found in conf/modules.config and Nextflow scripts.
• modules_config - CNAQC found in conf/modules.config and Nextflow scripts.
• modules_config - JOIN_CNAQC found in conf/modules.config and Nextflow scripts.
• modules_config - CTREE found in conf/modules.config and Nextflow scripts.
• modules_config - ANNOTATE_DRIVER found in conf/modules.config and Nextflow scripts.
• modules_config - ENSEMBLVEP_VEP found in conf/modules.config and Nextflow scripts.
• modules_config - ENSEMBLVEP_DOWNLOAD found in conf/modules.config and Nextflow scripts.
• modules_config - UNTAR found in conf/modules.config and Nextflow scripts.
• modules_config - CNA2CNAQC found in conf/modules.config and Nextflow scripts.
• modules_config - VCF2CNAQC found in conf/modules.config and Nextflow scripts.
• modules_config - CNAQC2TSV found in conf/modules.config and Nextflow scripts.
• modules_config - GET_POSITIONS_ALL found in conf/modules.config and Nextflow scripts.
• modules_config - GET_POSITIONS_REL found in conf/modules.config and Nextflow scripts.
• modules_config - JOIN_POSITIONS found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_MPILEUP found in conf/modules.config and Nextflow scripts.
• modules_config - MOBSTER found in conf/modules.config and Nextflow scripts.
• modules_config - PYCLONEVI found in conf/modules.config and Nextflow scripts.
• modules_config - SIGPROFILER found in conf/modules.config and Nextflow scripts.
• modules_config - SPARSE_SIGNATURES found in conf/modules.config and Nextflow scripts.
• modules_config - TINC found in conf/modules.config and Nextflow scripts.
• modules_config - VIBER found in conf/modules.config and Nextflow scripts.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
• nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 4.1.0
• rocrate_readme_sync - RO-Crate description matches the README.md.
• container_configs - conf/containers_conda_lock_files_amd64.config is up to date
• container_configs - conf/containers_conda_lock_files_arm64.config is up to date
• container_configs - conf/containers_docker_amd64.config is up to date
• container_configs - conf/containers_docker_arm64.config is up to date
• container_configs - conf/containers_singularity_https_amd64.config is up to date
• container_configs - conf/containers_singularity_https_arm64.config is up to date
• container_configs - conf/containers_singularity_oras_amd64.config is up to date
• container_configs - conf/containers_singularity_oras_arm64.config is up to date
• version_consistency - Version tags are consistent: manifest.version = 1.0.0, nfcore_yml.version = 1.0.0

Run details

• nf-core/tools version 4.1.0
• Run at 2026-10-08 08:16:30