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Add new component: gridss/call#12401

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imsarath:gridss_variantcall
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Add new component: gridss/call#12401
imsarath wants to merge 1 commit into
nf-core:masterfrom
imsarath:gridss_variantcall

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As part of the distributed computing GRIDSS subworkflow #4498, I added this gridss/call module. This module wraps the variant-calling step: it takes the per-sample preprocessed data and the assembly BAM (along with the input BAM/BAI files and reference genome), calls structural variants across the genome, and produces the final *.sv.gridss.vcf.gz.

PR checklist

Closes #4503

  • 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
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  • 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 marked this pull request as draft July 22, 2026 10:13
@imsarath imsarath changed the title added: new module gridss/call Add new component: gridss/call Jul 22, 2026
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new module: gridss/variantcall

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