Output phased variants by ljwharbers · Pull Request #141 · IntGenomicsLab/lrsomatic

ljwharbers · 2026-03-12T10:30:44Z

PR checklist

github-actions · 2026-03-12T10:32:48Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 8f2a771

+| ✅ 178 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗  28 tests had warnings |!

Details

❗ Test warnings:

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 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 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 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 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 meta.yml: #Add a description of the module and list keywords
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 - tumor_normal_happhase.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

❔ 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 manifest.version ends in dev: 1.1.0dev
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 - .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.
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'
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting_comment.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: 3.5.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-03-12 10:32:30

Copilot

Pull request overview

Enables publishing of LONGPHASE phased small-variant outputs so users get phased VCFs in the pipeline results directory.

Changes:

Configure LONGPHASE_PHASE to publish outputs under ${outdir}/${sample}/variants/phased.
Set a fixed ext.prefix for LONGPHASE_PHASE outputs.

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Copilot · 2026-03-12T10:33:53Z

    //

    withName: '.*:LONGPHASE_PHASE' {
+        ext.prefix = { "somatic_smallvariants" }


LONGPHASE_PHASE is used to phase germline/non-somatic SNVs (e.g., normals in subworkflows/local/tumor_normal_happhase.nf and the non-somatic VCF in tumor-only mode). Setting ext.prefix to somatic_smallvariants will label the published phased VCFs as somatic even when they are not, which is misleading for users and downstream tooling. Consider using a neutral prefix (e.g. phased_smallvariants) or include sample/type information in the prefix to accurately reflect the content.

Suggested change

ext.prefix = { "somatic_smallvariants" }

ext.prefix = { "phased_smallvariants" }

ljwharbers added 2 commits March 12, 2026 10:41

add publishdir for phase variants

36c449d

renamed phased variants output

8f2a771

Copilot AI review requested due to automatic review settings March 12, 2026 10:30

Copilot started reviewing on behalf of ljwharbers March 12, 2026 10:31 View session

Copilot AI reviewed Mar 12, 2026

View reviewed changes

ljwharbers requested review from robert-a-forsyth March 12, 2026 10:49

robert-a-forsyth approved these changes Mar 13, 2026

View reviewed changes

robert-a-forsyth merged commit 6847b59 into dev Mar 13, 2026
13 checks passed

ljwharbers deleted the output_phased_variants branch March 13, 2026 08:47

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Output phased variants#141

Output phased variants#141
robert-a-forsyth merged 2 commits into
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output_phased_variants

ljwharbers commented Mar 12, 2026

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✅ Tests passed:

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	ext.prefix = { "somatic_smallvariants" }
	ext.prefix = { "phased_smallvariants" }

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ljwharbers commented Mar 12, 2026

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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Pull request overview

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github-actions Bot commented Mar 12, 2026 •

edited

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️