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Add busco downloads as output #7210

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@dialvarezs dialvarezs commented Dec 12, 2024

This PR

  • Adds downloaded BUSCO lineages as an output.
  • Updates BUSCO version in busco/generateplot

PR checklist

  • 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

@dialvarezs dialvarezs marked this pull request as ready for review December 12, 2024 22:22
modules/nf-core/busco/busco/meta.yml Outdated Show resolved Hide resolved
modules/nf-core/busco/busco/meta.yml Outdated Show resolved Hide resolved
Comment on lines 87 to 88
"downloaded_lineages": [

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Is there a way to assert a bit more than empty?

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Seems like a lot of assertions just have empty results here in the snap.

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@dialvarezs dialvarezs Dec 13, 2024

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They come from the stub test, which only generates minimal outputs (nothing optional, and this process has plenty of them), and the snapshot includes the entire process output. I can adjust the snapshot to explicitly include only what was generated by the stub.

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Thank you for your review, I guess I addressed all the changes requested.

@dialvarezs dialvarezs requested a review from famosab December 13, 2024 18:35
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