fix clairs indel calling by robert-a-forsyth · Pull Request #99 · IntGenomicsLab/lrsomatic

robert-a-forsyth · 2025-10-30T16:11:08Z

PR checklist

Copilot

Pull Request Overview

This PR enhances the ClairS variant calling module to output separate VCF files for SNVs and indels in addition to the combined output, and increases the VEP process resource allocation.

Updated ClairS module to emit separate SNV and indel VCF outputs along with the combined VCF
Added ClairS command-line flags to enable indel calling and skip intermediate phasing
Changed VEP process label from process_medium to process_very_high

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.

File	Description
modules/local/clairs/main.nf	Modified output definitions to emit three separate VCF outputs (all_vcf, indel_vcf, snv_vcf) and added ClairS flags for indel calling and haplotagging
subworkflows/local/tumor_normal_happhase.nf	Updated to use the new `all_vcf` output channel instead of the generic `vcf` output
modules/nf-core/ensemblvep/vep/main.nf	Increased resource allocation from `process_medium` to `process_very_high`
tests/default.nf.test.snap	Updated test snapshots to include the new indel and snv VCF files, and reflected updated version/timestamp metadata

Comments suppressed due to low confidence (1)

modules/local/clairs/main.nf:59

The stub section only creates the combined VCF file (${prefix}.vcf.gz) but does not create the separate indel.vcf.gz and snv.vcf.gz files that are now expected outputs. The stub should create all three VCF files to match the updated output declarations.

    stub:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"

    """
    echo "" | gzip > ${prefix}.vcf.gz
    touch ${prefix}.vcf.gz.tbi

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        clairs: \$(/opt/bin/run_clairs  --version |& sed '1!d ; s/run_clairs //')
    END_VERSIONS
    """

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github-actions · 2025-10-30T16:13:16Z

`nf-core pipelines lint` overall result: Failed ❌

Posted for pipeline commit 29ec483

+| ✅ 174 tests passed       |+
#| ❔  25 tests were ignored |#
!| ❗ 157 tests had warnings |!
-| ❌   3 tests failed       |-

Details

❌ Test failures:

files_unchanged - .github/workflows/linting_comment.yml does not match the template
files_unchanged - .github/workflows/linting.yml does not match the template
files_unchanged - .prettierignore does not match the template

❗ Test warnings:

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: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
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: Fill in short bullet-pointed list of the default steps in the pipeline 2. Present QC for raw reads (MultiQC)
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 README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA 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 test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
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 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 usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
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
nextflow_config - Config variable ignored: validation.help.beforeText
nextflow_config - Config variable ignored: validation.help.afterText
nextflow_config - Config variable ignored: validation.summary.beforeText
nextflow_config - Config variable ignored: validation.summary.afterText
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
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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: validation.help.enabled
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 found: validation.help.command
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 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 manifest.version ends in dev: 1.0.0dev
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 - assets/email_template.html matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - .gitignore 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: 24.10.5, Config: 24.10.5
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: 3.3.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.3.2
Run at 2025-11-27 15:23:05

This reverts commit b20166f.

ljwharbers · 2025-11-20T17:16:33Z

-    tuple val(meta), path("*.vcf.gz"),      emit: vcf
-    tuple val(meta), path("*.vcf.gz.tbi"),  emit: tbi
-    path "versions.yml",                    emit: versions
+    tuple val(meta), path("${meta.id}.vcf.gz"),      emit: all_vcf


I think this will fail if someone sets a prefix with ext.prefix. Making the prefix globally accessible (removing def) and changing this to prefix should solve it (please test)

It looks like that prefix.vcf.gz is simply a symlink to snv.vcf.gz. So something is wonky here or is it me?

fix clairs indel calling

4c5973f

Copilot AI review requested due to automatic review settings October 30, 2025 16:11

Copilot AI reviewed Oct 30, 2025

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robert-a-forsyth added 3 commits November 18, 2025 11:34

view

d60b5ee

fix id

b20166f

remove view

233059a

robert-a-forsyth closed this Nov 18, 2025

robert-a-forsyth reopened this Nov 18, 2025

robert-a-forsyth added 7 commits November 18, 2025 19:09

Revert "fix id"

4350f57

This reverts commit b20166f.

revert

d3623ac

patch

424befd

prettier

c70e403

view

dadd850

grouptuple fix

e459367

remove nucleo arg

678dc48

robert-a-forsyth assigned ljwharbers Nov 20, 2025

ljwharbers added 3 commits November 20, 2025 18:17

change meta.id to prefix in CLAIRS`

eaf4cae

indentation

49d337e

remove view statement

484a091

ljwharbers requested changes Nov 20, 2025

View reviewed changes

robert-a-forsyth added 9 commits November 24, 2025 09:54

add view

200b95f

fix read-in

550ba65

fix read-in

afbb03a

fix read-in

ec83c21

fix read-in

339449a

merge + index clairS output

6bf8ee8

remove view

2c95ed2

adjust concat params

da63f26

add view

8af8469

robert-a-forsyth and others added 19 commits November 25, 2025 15:23

more view

9851c1f

view spelling

160eb79

fix channel logic

f746e65

lint

5b38eee

lint

dac7854

prettier

87bc148

fix channel meta

7cd7898

view

9e86276

fix multichannel

0d11cb9

edit view

4fcf630

change channel

800064f

remove view

be9e0ea

lint and snapshot

67f4be6

fix lint and snap

4b47c2f

fix log

ca04e17

whitespace

8881a18

formatting

2e2f4f3

formatting

d841fd1

add def back in

29ec483

ljwharbers approved these changes Nov 27, 2025

View reviewed changes

robert-a-forsyth merged commit 759accc into dev Nov 27, 2025
4 of 6 checks passed

robert-a-forsyth deleted the clairs_fix branch November 28, 2025 12:11

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fix clairs indel calling#99

fix clairs indel calling#99
robert-a-forsyth merged 42 commits into
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clairs_fix

robert-a-forsyth commented Oct 30, 2025

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github-actions Bot commented Oct 30, 2025 •

edited

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❌ Test failures:

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✅ Tests passed:

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robert-a-forsyth commented Oct 30, 2025

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nf-core pipelines lint overall result: Failed ❌

❌ Test failures:

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✅ Tests passed:

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github-actions Bot commented Oct 30, 2025 •

edited

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`nf-core pipelines lint` overall result: Failed ❌