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Update BCFTOOLS/ISEC: additional arguments #9766

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Update BCFTOOLS/ISEC: additional arguments #9766

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@georgiakes georgiakes commented Jan 23, 2026 •
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PR checklist

Closes #9764

  • 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

itrujnara
itrujnara reviewed Jan 26, 2026
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Hi, everything looks fine here, but one test is missing.

modules/nf-core/bcftools/isec/tests/main.nf.test
}
}

test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - regions - stub") {
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I don't see a test for the file_list input. Can you please add one? You can generate the list on the fly with a setup block if needed.

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georgiakes commented Jan 27, 2026

Should I also update tests to fix linting? It fails because the output files are empty.

itrujnara
itrujnara approved these changes Jan 27, 2026
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The code looks fine now. Please fix the linting, making sure that files are only empty in stub tests.

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update module: BCFTOOLS/ISEC

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