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Merge BAM_SOMATIC_VARIANT_CALLING_GATK subworkflows - #13335

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Merge BAM_SOMATIC_VARIANT_CALLING_GATK subworkflows#13335
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@beatrizsavinhas beatrizsavinhas commented Oct 16, 2026 •
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Create BAM_SOMATIC_VARIANT_CALLING_GATK subworkflow merging the logic for BAM_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING_GATK and BAM_TUMOR_ONLY_SOMATIC_VARIANT_CALLING_GATK. A single subworkflow capable of performing both analysis types reduces code duplication in pipelines that can run both tumor only and tumor-normal analyses.

  • This comment contains a description of changes (with reason).
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  • If necessary, include test data in your PR.
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  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@beatrizsavinhas beatrizsavinhas self-assigned this Oct 19, 2026
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github-actions Bot commented Oct 21, 2026

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This PR exceeds the recommended size of 1000 lines. Please make sure you are NOT addressing multiple issues with one PR. Note this PR might be rejected due to its size.

@github-actions github-actions Bot removed the size/l label Oct 21, 2026
@beatrizsavinhas
beatrizsavinhas marked this pull request as ready for review October 21, 2026 11:23
@github-actions github-actions Bot added size/l and removed size/xl labels Oct 26, 2026
@github-actions github-actions Bot added size/xl and removed size/l labels Oct 29, 2026
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github-actions Bot commented Oct 29, 2026

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This PR exceeds the recommended size of 1000 lines. Please make sure you are NOT addressing multiple issues with one PR. Note this PR might be rejected due to its size.

@maxulysse maxulysse mentioned this pull request Oct 29, 2026
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@beatrizsavinhas

beatrizsavinhas commented Oct 29, 2026 •
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As per your suggestion @imsarath, the previous subworkflows have now been deprecated instead of removed.
While doing this, I found that the instructions for deprecating components needed adjustments for subworkflows so I opened this PR to address that: nf-core/website#4511

beatrizsavinhas
beatrizsavinhas commented Oct 30, 2026
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Comment thread subworkflows/nf-core/bam_somatic_variant_calling_gatk/main.nf
Comment on lines +95 to +113
ch_calculatecontamination_in = GATK4_GETPILEUPSUMMARIES.out.table
.map { meta, table ->
tuple(
meta.original_meta,
[(meta.id.endsWith('_tumor') ? 'tumor' : 'normal'): table]
)
}
.groupTuple()
// Ensure the correct order of the tables (tumor first, normal second)
.map { meta, table_maps ->

def tables = table_maps.sum([:])

tuple(
meta,
tables.tumor,
tables.normal ? tables.normal : []
)
}

@beatrizsavinhas beatrizsavinhas Oct 30, 2026

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I think this logic could be improved and simplified! Any suggestions?

@FriederikeHanssen

FriederikeHanssen commented Nov 2, 2026

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I just had to pull apart the mutect2 subworkflow to move the filtering in into a different subworkflow so it can be shared with other callers, in case this is useful for you : nf-core/sarek#2349

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@imsarath imsarath Awaiting requested review from imsarath

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@beatrizsavinhas @FriederikeHanssen @imsarath