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Add subworkflow for gridss somatic structural variant calling - #12574

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imsarath wants to merge 3 commits into
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imsarath:subworkflow_gridss_somatic_svs_calling
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Add subworkflow for gridss somatic structural variant calling#12574
imsarath wants to merge 3 commits into
nf-core:masterfrom
imsarath:subworkflow_gridss_somatic_svs_calling

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@imsarath

@imsarath imsarath commented Aug 4, 2026

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This PR adds bam_tumor_normal_somatic_structural_variant_calling_gridss, a subworkflow that calls somatic structural variants from a tumor/normal BAM pair. It chains the full GRIDSS workflow - optional targeted fragment extraction, per-sample preprocess, joint assembly and call, then gridss_somatic_filter. It emits the unfiltered joint VCF plus the all-somatic and high-confidence somatic call sets.

PR checklist

Closes #4498

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • 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

@imsarath imsarath self-assigned this Aug 4, 2026
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new subworkflow: distributed computing GRIDSS subworkflow

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