Dev

[robert-a-forsyth]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[Copilot]

Pull request overview

This pull request adds multiple nf-core modules to the pipeline, including tools for alignment (minimap2), variant calling/structural variant detection (severus, longphase), quality control (samtools, mosdepth, multiqc), methylation analysis (modkit), compression utilities (pigz, untar), and variant manipulation (bcftools). The changes appear to be focused on expanding the pipeline's capabilities for long-read somatic variant analysis.

• Adds 15+ new nf-core module implementations
• Includes comprehensive test suites with nf-test for all new modules
• Updates module versions (e.g., multiqc 1.25.1 → 1.32, samtools to 1.21)

Reviewed changes

Copilot reviewed 220 out of 259 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
modules/nf-core/severus/*	Adds severus module (v1.6) for somatic SV calling with updated inputs/outputs
modules/nf-core/untar/*	Adds untar module for archive extraction
modules/nf-core/samtools/*	Adds samtools submodules (stats, index, idxstats, flagstat, faidx, cat)
modules/nf-core/mosdepth/*	Adds mosdepth module for sequencing coverage calculation
modules/nf-core/multiqc/*	Updates multiqc from v1.25.1 to v1.32
modules/nf-core/modkit/pileup/*	Adds modkit pileup module for methylation analysis
modules/nf-core/minimap2/*	Adds minimap2 align and index modules
modules/nf-core/pigz/uncompress/*	Adds pigz uncompress module for parallel decompression
modules/nf-core/longphase/*	Adds longphase configuration files for phasing
modules/nf-core/bcftools/merge/*	Adds bcftools merge configuration

---

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[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0c99122

+| ✅ 176 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗ 147 tests had warnings |!

Details

❗ Test warnings:

• nextflow_config - Config manifest.version should end in dev: 1.0.0
• readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
• pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
• pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in lint_log.txt: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in lint_log.txt: List additional required output channels/values here
• pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
• pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
• pipeline_todos - TODO string in base.config: Check the defaults for all processes
• pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
• pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
• pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
• pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
• pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
• pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
• pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
• pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
• pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
• pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
• pipeline_todos - TODO string in main.nf: List required Conda package(s).
• pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
• pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
• pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
• pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in main.nf: List additional required output channels/values here
• pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
• pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
• pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
• pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
• pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
• pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
• pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
• pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
• pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
• pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
• pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
• pipeline_todos - TODO string in main.nf: List required Conda package(s).
• pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
• pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
• pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
• pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in main.nf: List additional required output channels/values here
• pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
• pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
• pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
• pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
• pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
• pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
• pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
• pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
• pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
• pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
• pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
• pipeline_todos - TODO string in main.nf: List required Conda package(s).
• pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
• pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
• pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
• pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in main.nf: List additional required output channels/values here
• pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
• pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
• pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
• pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
• pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
• pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
• pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
• pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
• pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
• pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
• pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
• pipeline_todos - TODO string in main.nf: List required Conda package(s).
• pipeline_todos - TODO string in main.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
• pipeline_todos - TODO string in main.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
• pipeline_todos - TODO string in main.nf: Where applicable please provide/convert compressed files as input/output
• pipeline_todos - TODO string in main.nf: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in main.nf: List additional required output channels/values here
• pipeline_todos - TODO string in main.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
• pipeline_todos - TODO string in main.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
• pipeline_todos - TODO string in main.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
• pipeline_todos - TODO string in main.nf: Please replace the example samtools command below with your module's command
• pipeline_todos - TODO string in main.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
• pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
• pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
• pipeline_todos - TODO string in main.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
• pipeline_todos - TODO string in main.nf: A module file SHOULD only define input and output files as command-line parameters.
• pipeline_todos - TODO string in main.nf: Software that can be piped together SHOULD be added to separate module files
• pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
• pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
• pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
• pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
• pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
• local_component_structure - tumor_only_happhase.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - prepare_annotation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - prepare_reference_files.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - tumor_normal_happhase.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: assets/nf-core-lrsomatic_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-lrsomatic_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-lrsomatic_logo_dark.png
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
• files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File ignored due to lint config: assets/email_template.txt
• files_unchanged - File ignored due to lint config: assets/nf-core-lrsomatic_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-lrsomatic_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-lrsomatic_logo_dark.png
• files_unchanged - File ignored due to lint config: docs/README.md
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/lrsomatic/lrsomatic/.github/workflows/awstest.yml
• schema_params - schema_params

✅ 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: 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/CONTRIBUTING.md
• files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.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/linting_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: conf/modules.config
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• 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: 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-lrsomatic_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/WorkflowLrsomatic.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.nextflowVersion
• nextflow_config - Config variable found: manifest.description
• nextflow_config - Config variable found: manifest.version
• 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 dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• 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.igenomes_base= s3://ngi-igenomes/igenomes/
• nextflow_config - Config default value correct: params.save_secondary_alignment= true
• nextflow_config - Config default value correct: params.ascat_penalty= 150
• nextflow_config - Config default value correct: params.ascat_min_base_qual= 20
• nextflow_config - Config default value correct: params.ascat_min_counts= 10
• nextflow_config - Config default value correct: params.ascat_min_map_qual= 10
• nextflow_config - Config default value correct: params.ascat_longread_bins= 2000
• nextflow_config - Config default value correct: params.ascat_allelecounter_flags= -f 0
• 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.publish_dir_mode= copy
• nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
• nextflow_config - Config default value correct: params.validate_params= true
• 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.normal_fiber= true
• 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 - LICENSE matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/workflows/branch.yml matches the template
• files_unchanged - .github/workflows/linting_comment.yml matches the template
• files_unchanged - .github/workflows/linting.yml matches the template
• files_unchanged - assets/email_template.html matches the template
• files_unchanged - assets/sendmail_template.txt 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
• readme - README Nextflow minimum version badge matched config. Badge: 25.04.0, Config: 25.04.0
• readme - README nf-core template version badge found.
• 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'
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: clean-up.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 'export_plots: true'.
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• local_component_structure - local modules directory structure is correct 'modules/local/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• modules_config - conf/modules.config found and not ignored.
• modules_config - ENSEMBLVEP_DOWNLOAD 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: 3.5.1
• rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

• nf-core/tools version 3.5.1
• Run at 2025-11-28 13:56:01