Deepvariant by robert-a-forsyth · Pull Request #149 · IntGenomicsLab/lrsomatic

robert-a-forsyth · 2026-03-24T11:58:38Z

PR checklist

Copilot

Pull request overview

This PR integrates DeepVariant (and DeepSomatic) into the lrsomatic pipeline and refactors small-variant calling / phasing logic by splitting former happhase subworkflows into dedicated tumor-only, paired, consensus, and phasing components. It also adds multiple nf-core module implementations (bcftools helpers, DeepVariant processes) plus nf-test coverage for the new modules/subworkflow.

Changes:

Refactor LRSOMATIC small-variant calling into new subworkflows (tumor-only, paired germline/somatic, consensus, phasing/haplotyping) and wire outputs into downstream steps (VEP/Severus).
Add nf-core DeepVariant subworkflow and its component processes (makeexamples/callvariants/postprocessvariants) with tests.
Introduce bcftools helper modules (norm/isec/query/annotate) and config wiring (including GPU toggle via params.use_gpu).

Reviewed changes

Copilot reviewed 93 out of 94 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
workflows/lrsomatic.nf	Rewires pipeline to new small-variant subworkflows and PoN handling.
subworkflows/nf-core/deepvariant/main.nf	Adds DeepVariant subworkflow wrapper around makeexamples/callvariants/postprocessvariants.
subworkflows/nf-core/deepvariant/meta.yml	Defines DeepVariant subworkflow I/O contract.
subworkflows/nf-core/deepvariant/README.md	Documents DeepVariant subworkflow usage and metadata-uniqueness requirement.
subworkflows/nf-core/deepvariant/deepvariant.diff	Patch tracking for nf-core DeepVariant subworkflow.
subworkflows/nf-core/deepvariant/tests/main.nf.test	Adds nf-test coverage for DeepVariant subworkflow.
subworkflows/nf-core/deepvariant/tests/main.nf.test.snap	Snapshot outputs for DeepVariant subworkflow tests.
subworkflows/nf-core/deepvariant/tests/equality.nf.test	Adds equality test comparing subworkflow vs `DEEPVARIANT_RUNDEEPVARIANT` process.
subworkflows/nf-core/deepvariant/tests/deepvariant-workflow-and-process-equality-tester.nf	Helper workflow to run both implementations and emit comparable outputs.
subworkflows/nf-core/deepvariant/tests/nextflow.config	Test-specific DeepVariant args configuration.
subworkflows/nf-core/deepvariant/tests/disable-small-model.conf	Test config to disable small-model generation.
subworkflows/local/tumor_only_happhase.nf	Removes prior tumor-only happhase implementation.
subworkflows/local/tumor_normal_happhase.nf	Removes prior paired (tumor-normal) happhase implementation.
subworkflows/local/tumor_only/tumoronly_smallvar.nf	New tumor-only small-variant calling (ClairS-TO / DeepVariant / DeepSomatic + consensus selection).
subworkflows/local/paired/paired_smallvar_germline.nf	New paired germline calling (Clair3 / DeepVariant + consensus selection).
subworkflows/local/paired/paired_smallvar_somatic.nf	New paired somatic calling (ClairS / DeepSomatic + consensus selection).
subworkflows/local/small_variant_consensus.nf	Adds consensus/all-variants merging logic using bcftools modules.
subworkflows/local/phasing_haplotyping.nf	Adds unified phasing/haplotyping + (optional) modcall flow for tumor-only and paired samples.
subworkflows/local/deepsomatic.nf	Adds DeepSomatic subworkflow wrapper (makeexamples/callvariants/postprocessvariants).
nextflow.config	Adds new pipeline params (`germline_var_keep`, `somatic_var_keep`, `trust_caller`, `use_gpu`, `skip_modcall`, PoN params).
nextflow_schema.json	Adds schema block for small-variant calling options.
conf/modules.config	Adds process-level config for new modules/subworkflows (DeepVariant, DeepSomatic, bcftools helpers, LongPhase split).
conf/test.config	Adds test-profile overrides to constrain regions for DeepVariant/DeepSomatic.
conf/base.config	Updates GPU configuration to be driven by `params.use_gpu`.
modules.json	Registers newly added nf-core modules/subworkflow and patch files.
.gitignore	Ignores `out/` directory.
modules/nf-core/deepvariant/makeexamples/main.nf	Adds/patches DeepVariant makeexamples (incl. `--sample_name`).
modules/nf-core/deepvariant/makeexamples/meta.yml	Adds DeepVariant makeexamples module metadata.
modules/nf-core/deepvariant/makeexamples/deepvariant-makeexamples.diff	Patch tracking for DeepVariant makeexamples module.
modules/nf-core/deepvariant/makeexamples/tests/nextflow.config	Test configuration for DeepVariant makeexamples.
modules/nf-core/deepvariant/makeexamples/tests/main.nf.test	nf-test coverage for DeepVariant makeexamples.
modules/nf-core/deepvariant/makeexamples/tests/main.nf.test.snap	Snapshots for DeepVariant makeexamples tests.
modules/nf-core/deepvariant/callvariants/main.nf	Adds/patches DeepVariant callvariants (GPU/noaccel label selection).
modules/nf-core/deepvariant/callvariants/meta.yml	Adds DeepVariant callvariants module metadata.
modules/nf-core/deepvariant/callvariants/deepvariant-callvariants.diff	Patch tracking for DeepVariant callvariants module.
modules/nf-core/deepvariant/callvariants/tests/nextflow.config	Test configuration for DeepVariant callvariants.
modules/nf-core/deepvariant/callvariants/tests/main.nf.test	nf-test coverage for DeepVariant callvariants.
modules/nf-core/deepvariant/callvariants/tests/main.nf.test.snap	Snapshots for DeepVariant callvariants tests.
modules/nf-core/deepvariant/postprocessvariants/main.nf	Adds/patches DeepVariant postprocessvariants (incl. `--sample_name`).
modules/nf-core/deepvariant/postprocessvariants/meta.yml	Adds DeepVariant postprocessvariants module metadata.
modules/nf-core/deepvariant/postprocessvariants/deepvariant-postprocessvariants.diff	Patch tracking for DeepVariant postprocessvariants module.
modules/nf-core/deepvariant/postprocessvariants/tests/nextflow.config	Test configuration for DeepVariant postprocessvariants.
modules/nf-core/deepvariant/postprocessvariants/tests/main.nf.test	nf-test coverage for DeepVariant postprocessvariants.
modules/nf-core/deepvariant/postprocessvariants/tests/main.nf.test.snap	Snapshots for DeepVariant postprocessvariants tests.
modules/nf-core/bcftools/norm/main.nf	Adds bcftools norm module used for normalization and indexing logic.
modules/nf-core/bcftools/norm/meta.yml	Metadata for bcftools norm module.
modules/nf-core/bcftools/norm/environment.yml	Conda env for bcftools norm module.
modules/nf-core/bcftools/norm/tests/nextflow.config	Test defaults for bcftools norm.
modules/nf-core/bcftools/norm/tests/nextflow.vcf.config	Test config for VCF output mode.
modules/nf-core/bcftools/norm/tests/nextflow.vcf_gz.config	Test config for VCF.GZ output mode.
modules/nf-core/bcftools/norm/tests/nextflow.bcf.config	Test config for BCF output mode.
modules/nf-core/bcftools/norm/tests/nextflow.bcf_gz.config	Test config for BCF.GZ output mode.
modules/nf-core/bcftools/norm/tests/vcf_gz_index.config	Test config for default index writing.
modules/nf-core/bcftools/norm/tests/vcf_gz_index_tbi.config	Test config for TBI index writing.
modules/nf-core/bcftools/norm/tests/vcf_gz_index_csi.config	Test config for CSI index writing.
modules/nf-core/bcftools/isec/main.nf	Adds bcftools isec module with extra emitted outputs for consensus/private sets.
modules/nf-core/bcftools/isec/meta.yml	Metadata for bcftools isec module.
modules/nf-core/bcftools/isec/environment.yml	Conda env for bcftools isec module.
modules/nf-core/bcftools/isec/bcftools-isec.diff	Patch tracking for bcftools isec module.
modules/nf-core/bcftools/isec/tests/nextflow.config	Test args for bcftools isec module.
modules/nf-core/bcftools/isec/tests/main.nf.test	nf-test coverage for bcftools isec module.
modules/nf-core/bcftools/isec/tests/main.nf.test.snap	Snapshots for bcftools isec tests.
modules/nf-core/bcftools/query/main.nf	Adds bcftools query module that bgzips + tabix-indexes output.
modules/nf-core/bcftools/query/meta.yml	Metadata for bcftools query module.
modules/nf-core/bcftools/query/environment.yml	Conda env for bcftools query module.
modules/nf-core/bcftools/query/bcftools-query.diff	Patch tracking for bcftools query module.
modules/nf-core/bcftools/query/tests/nextflow.config	Test args for bcftools query module.
modules/nf-core/bcftools/query/tests/main.nf.test	nf-test coverage for bcftools query module.
modules/nf-core/bcftools/query/tests/main.nf.test.snap	Snapshots for bcftools query tests.
modules/nf-core/bcftools/annotate/main.nf	Adds bcftools annotate module (annotate + output type/index handling).
modules/nf-core/bcftools/annotate/meta.yml	Metadata for bcftools annotate module.
modules/nf-core/bcftools/annotate/environment.yml	Conda env for bcftools annotate module.
modules/nf-core/bcftools/annotate/tests/nextflow.config	Test config for bcftools annotate module.
modules/nf-core/bcftools/annotate/tests/main.nf.test.snap	Snapshots for bcftools annotate tests.
modules/nf-core/bcftools/merge/main.nf	Adjusts bcftools merge input signature for fasta/fai separation.
modules/nf-core/bcftools/merge/bcftools-merge.diff	Patch tracking for bcftools merge input change.
modules/nf-core/longphase/phase/main.nf	Adjusts tabix indexing to handle multiple LongPhase outputs.
modules/nf-core/severus/main.nf	Fixes output filename patterns (breakpoint(s) naming).
modules/local/clairsto/main.nf	Updates ClairS-TO module to accept PoN VCFs/flags and set `--sample_name`.
modules/local/clairs/main.nf	Adds `--sample_name` support via prefix.
modules/local/clair3/main.nf	Adds GPU/noaccel label and passes `--sample_name`.
modules/local/vcfsplit/main.nf	Updates non-somatic filtering expression before constructing germline VCF.
modules/local/longphase/modcall/main.nf	Adds LongPhase modcall module.
modules/local/fibertoolsrs/predictm6a/main.nf	Adds GPU/noaccel label selection.
modules/local/fibertoolsrs/nucleosomes/main.nf	Adds GPU/noaccel label selection.
modules/local/fibertoolsrs/fire/main.nf	Adds GPU/noaccel label selection.
modules/local/deepsomatic/makeexamples/main.nf	Adds DeepSomatic makeexamples module.
modules/local/deepsomatic/callvariants/main.nf	Adds DeepSomatic callvariants module (GPU/noaccel label selection).
modules/local/deepsomatic/postprocessvariants/main.nf	Adds DeepSomatic postprocessvariants module.

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…o deepvariant

github-actions · 2026-03-24T13:59:14Z

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

Posted for pipeline commit deefcf9

+| ✅ 208 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗  34 tests had warnings |!

Details

❗ Test warnings:

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 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 meta.yml: #Add a description of the module and list keywords
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
schema_description - No description provided in schema for parameter: autocorrelation
schema_description - No description provided in schema for parameter: vep_custom
schema_description - No description provided in schema for parameter: vep_custom_tbi
schema_description - No description provided in schema for parameter: severus_minsupport
schema_description - No description provided in schema for parameter: wakhan_chroms
local_component_structure - prepare_reference_files.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - deepsomatic.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - phasing_haplotyping.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 - small_variant_consensus.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.germline_var_combine= all
nextflow_config - Config default value correct: params.somatic_var_combine= all
nextflow_config - Config default value correct: params.prioritize_caller_germline= deepvariant
nextflow_config - Config default value correct: params.prioritize_caller_somatic= deepsomatic
nextflow_config - Config default value correct: params.igenomes_ignore= false
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.vep_cache= s3://annotation-cache/vep_cache/
nextflow_config - Config default value correct: params.vep_args= --everything --filter_common --per_gene --total_length --offline --format vcf
nextflow_config - Config default value correct: params.vep_cache_version= 113
nextflow_config - Config default value correct: params.download_vep_cache= false
nextflow_config - Config default value correct: params.severus_minsupport= 3
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.ascat_pdf_plots= false
nextflow_config - Config default value correct: params.skip_qc= false
nextflow_config - Config default value correct: params.skip_cramino= false
nextflow_config - Config default value correct: params.skip_mosdepth= false
nextflow_config - Config default value correct: params.skip_bamstats= false
nextflow_config - Config default value correct: params.skip_wakhan= false
nextflow_config - Config default value correct: params.skip_fiber= false
nextflow_config - Config default value correct: params.skip_ascat= false
nextflow_config - Config default value correct: params.skip_m6a= false
nextflow_config - Config default value correct: params.skip_vep= false
nextflow_config - Config default value correct: params.skip_normalfiber= false
nextflow_config - Config default value correct: params.skip_nanoplot= false
nextflow_config - Config default value correct: params.skip_whatshapstats= false
nextflow_config - Config default value correct: params.skip_modcall= false
nextflow_config - Config default value correct: params.use_gpu= false
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.version= false
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.plaintext_email= false
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.monochrome_logs= false
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.help= false
nextflow_config - Config default value correct: params.help_full= false
nextflow_config - Config default value correct: params.show_hidden= false
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: download_pipeline.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.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: 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: 3.5.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-03-31 17:02:14

robert-a-forsyth added 18 commits March 12, 2026 14:16

install deepvariant subworkflow

f99d4d2

add deepsomatic

12869b0

get deepvariant running

388d180

add deep somatic and split processes for more efficent gpu requests

af3a58e

add gpu process labels for deepvariant, clair3, fibertools

ba8cf59

install helpful bcftools modules for consensus vcfs

8045134

bcftools query

a5ca08a

preliminary small variant consensus calling stuff

20437ff

fix channel structure

0ac7404

Merge branch 'dev' into deepvariant

5910df7

preliminary germline merging channel structure

c3635d8

fix bcftool merge input to stop value channel conversion

713b11a

channel revision

5747283

channel restructure

f676fd4

improve clairsto pon handling

43ca8f8

migrate some functions to different workflows to improve readability

5fda744

somatic phasing

ad88f88

gpu optional flag, and snap updates

7e414e0

Copilot AI review requested due to automatic review settings March 24, 2026 11:58

Copilot started reviewing on behalf of robert-a-forsyth March 24, 2026 11:59 View session

Copilot AI reviewed Mar 24, 2026

View reviewed changes

robert-a-forsyth and others added 7 commits March 24, 2026 13:17

merging fixes

47194e1

Update modules/local/vcfsplit/main.nf

e098f3a

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update modules/nf-core/bcftools/isec/main.nf

abf274f

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

small fixes

c932ea4

update snap

bf44b0a

Merge branch 'deepvariant' of github.com:IntGenomicsLab/lrsomatic int…

fb2f842

…o deepvariant

prettier

e5d8ae6

repatch isec

69a8edd

robert-a-forsyth and others added 8 commits March 24, 2026 15:07

repatch bcftools query

3e66078

fixed co-pilot fix

bcb68a1

fix value channel

eff9257

fixed severus channel

00be26e

fix snap and change modcall label

ee028d3

fix channel structure, update longphase

48a71f6

fix longphase output

fcf2547

small changes

6f5a1b1

ljwharbers reviewed Mar 27, 2026

View reviewed changes

robert-a-forsyth added 4 commits March 27, 2026 14:28

revert longphase output versions

eb86f4a

adressing comments

f094a0b

updates to documentation/process labels

4834e8c

prettier

5cfadfb

ljwharbers approved these changes Mar 30, 2026

View reviewed changes

documentation, small fixes to config

deefcf9

robert-a-forsyth merged commit d2cc09b into dev Mar 31, 2026
7 checks passed

ljwharbers deleted the deepvariant branch April 22, 2026 14:11

Copilot AI mentioned this pull request May 19, 2026

added changelog and docs #162

Merged

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robert-a-forsyth commented Mar 24, 2026

PR checklist

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github-actions Bot commented Mar 24, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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github-actions Bot commented Mar 24, 2026 •

edited

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