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New module: gtdbtk/gtdbtoncbimajorityvote #8389

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@prototaxites prototaxites commented May 2, 2025

Adds a new module: gtdbtk/gtdbtoncbimajorityvote

This requires a couple of changes to the gtdbtk/classifywf module:

  • The new module takes as input the files from classifywf, and requires that the structure be as-is. So I've removed the code that re-arranges and tidies up the classifywf outputs
  • I've added a new output that outputs everything from gtdbtk/classifywf
  • Harshill alignment ☺️
  • Bump version to 2.4.1

For the new module, one of the inputs is the prefix used in the gtdbtk/classifywf run - I'm currently just inferring this from the input files. But it could be an explicit input if anyone thinks that's better

Note: It would be good to move the mockup database to somewhere in the nf-core test data sphere, as the download speed is in the range of a handful of kbps.

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

@prototaxites prototaxites requested a review from jfy133 May 2, 2025 14:36
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@jfy133 Since you added the tests the other day - better to leave the empty file in the classifywf test despite causing a lint failure?

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