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Add new module gatk4/nvscorevariants

Open famosab opened this issue 7 months ago • 1 comments

PR checklist

Closes #XXX

  • [ ] 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.
  • [ ] Emit the versions.yml file.
  • [ ] 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

GATK modules were bumped in #6917 but this one fell through

famosab avatar May 28 '25 14:05 famosab

The new module does not work for now because of: https://github.com/broadinstitute/gatk/issues/9190

famosab avatar May 28 '25 15:05 famosab