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Specify allosomal contigs in PostprocessGermlineCNVCalls (GATK) - #966

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benstory wants to merge 3 commits into
nf-core:devfrom
benstory:fix/gatkCNVparam
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Specify allosomal contigs in PostprocessGermlineCNVCalls (GATK)#966
benstory wants to merge 3 commits into
nf-core:devfrom
benstory:fix/gatkCNVparam

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@benstory

@benstory benstory commented Aug 6, 2026 •
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Description

PostprocessGermlineCNVCalls currently runs without --allosomal-contig.
Per the GATK documentation, any contig not declared as allosomal is assumed
to be autosomal and given the reference copy-number set by
--autosomal-ref-copy-number (default 2). This means X and Y are genotyped
against a diploid reference regardless of the sample's karyotype, so male
samples get spurious DEL calls across X and Y, and female samples get
spurious calls on Y.

Passing --allosomal-contig lets GATK take the reference copy-number for
those contigs from the contig ploidy calls produced by
DetermineGermlineContigPloidy, which is what the tool expects.

Ref: https://gatk.broadinstitute.org/hc/en-us/articles/360036366292-PostprocessGermlineCNVCalls

Changes

  • Added --allosomal-contig to ext.args for the postprocessing step in
    conf/modules/call_sv_germlinecnvcaller.config.
  • Contig naming is selected from params.genome, following the pattern
    already used for --haploid_contigs in
    conf/modules/call_snv_deepvariant.config: X/Y for GRCh37 and
    chrX/chrY otherwise.

Fixes #965

PR checklist

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

Ben Story
Merge pull request nf-core#962 from nf-core/issue930-upd-rhocallviz-u…
550b570 
…nfiltered

Feed UPD/rhocall-viz unfiltered vcfanno output instead of the VEP-filtered VCF
@github-actions

github-actions Bot commented Aug 6, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@github-actions

github-actions Bot commented Aug 6, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f16a302

+| ✅ 257 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   9 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ mq_metrics = SENTIEON_DATAMETRICS.out.mq_metrics.ifEmpty(null) // channel: [ val(meta), path(mq_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ qd_metrics = SENTIEON_DATAMETRICS.out.qd_metrics.ifEmpty(null) // channel: [ val(meta), path(qd_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ gc_metrics = SENTIEON_DATAMETRICS.out.gc_metrics.ifEmpty(null) // channel: [ val(meta), path(gc_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ gc_summary = SENTIEON_DATAMETRICS.out.gc_summary.ifEmpty(null) // channel: [ val(meta), path(gc_summary) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ aln_metrics = SENTIEON_DATAMETRICS.out.aln_metrics.ifEmpty(null) // channel: [ val(meta), path(aln_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ is_metrics = SENTIEON_DATAMETRICS.out.is_metrics.ifEmpty(null) // channel: [ val(meta), path(is_metrics) ]
    _
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.3
  • Run at 2026-08-06 14:44:12

@ramprasadn

ramprasadn commented Aug 24, 2026

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Hi @benstory, just realized that I responded to you in a comment on your issue rather than here in the PR. Your suggestion below, which should enable it for all samples regardless of sex, sounds good to me.

ext.args = { params.genome == 'GRCh37' ? '--allosomal-contig X --allosomal-contig Y' : '--allosomal-contig chrX --allosomal-contig chrY' }

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@benstory @ramprasadn