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Pull request overview
Adds a WhatsHap stats QC step to the lrsomatic workflow (with a skip flag) and wires the resulting TSV into MultiQC. The PR also includes additional nf-core module content for DeepVariant (modules + nf-test configs/snapshots).
Changes:
- Integrate
WHATSHAP_STATSintoworkflow LRSOMATIC, collecting outputs into MultiQC and addingskip_whatshapstats. - Update tumor-only and tumor/normal happhase subworkflows to use
LONGPHASE_PHASE.out.snv_vcffor the germline VEP channel. - Add nf-core modules/tests for
whatshap/statsand DeepVariant (makeexamples,callvariants,postprocessvariants) plusmodules.jsonupdates.
Reviewed changes
Copilot reviewed 28 out of 28 changed files in this pull request and generated 10 comments.
Show a summary per file
| File | Description |
|---|---|
| workflows/lrsomatic.nf | Imports and conditionally runs WHATSHAP_STATS; mixes TSV into MultiQC inputs. |
| subworkflows/local/tumor_only_happhase.nf | Switches germline VEP input to phased VCF from LongPhase. |
| subworkflows/local/tumor_normal_happhase.nf | Switches germline VEP input to phased VCF from LongPhase (comment now slightly outdated). |
| nextflow.config | Adds default params.skip_whatshapstats. |
| nextflow_schema.json | Adds schema entry for skip_whatshapstats. |
| conf/modules.config | Adds publishDir/args/prefix defaults for WHATSHAP_STATS; also adds --sample_name args for Clair modules. |
| modules/nf-core/whatshap/stats/* | New nf-core-style module + metadata + tests for WhatsHap stats. |
| modules/nf-core/deepvariant/* (+ tests) | Adds DeepVariant modules and nf-test scaffolding/snapshots. |
| modules.json | Records installed nf-core modules including whatshap/stats (and nanoplot entry update). |
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workflows/lrsomatic.nf
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| include { ENSEMBLVEP_VEP as SOMATIC_VEP } from '../modules/nf-core/ensemblvep/vep/main.nf' | ||
| include { ENSEMBLVEP_VEP as GERMLINE_VEP } from '../modules/nf-core/ensemblvep/vep/main.nf' | ||
| include { ENSEMBLVEP_VEP as SV_VEP } from '../modules/nf-core/ensemblvep/vep/main.nf' | ||
| include { WHATSHAP_STATS } from '../modules/nf-core/whatshap/stats/main' |
| type: boolean | ||
| description: Whether to include GTF output file | ||
| default: false | ||
| - inlude_block_output: |
| return [meta, vcf, extra] | ||
| } | ||
| .set { germline_vep } | ||
| // [meta, clair3_vcf, []] -- germline small variants for VEP annotation |
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| ontologies: [] | ||
| - - meta5: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing reference information | ||
| e.g. [ id:'genome' ] | ||
| pattern: "*.gzi" |
| type: string | ||
| description: The name of the tool | ||
| - whatshap --version: | ||
| type: string |
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| process DEEPVARIANT_MAKEEXAMPLES { | ||
| tag "$meta.id" | ||
| label 'process_high' | ||
|
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||
| //Conda is not supported at the moment | ||
| container "docker.io/google/deepvariant:1.9.0" |
| - vcf: | ||
| type: file | ||
| description: Phased variant vcf file | ||
| pattern: "*.vcf" |
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| val(include_tsv_output) // value: [ true | false ] | ||
| val(include_gtf_output) // value: [ true | false ] | ||
| val(inlude_block_output) // value: [ true | false ] | ||
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| pattern: "*.bam/cram" | ||
| ontologies: [] | ||
| - index: | ||
| type: file | ||
| description: Index of BAM/CRAM file | ||
| pattern: "*.bai/crai" |
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
robert-a-forsyth
approved these changes
Mar 17, 2026
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).