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New module that produces predicted phylogenetic trees from multiple sequence alignment files (both for DNA and Amino Acids)

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

"""
input[0] = [
[ id:'test_aa' ],
file(params.modules_testdata_base_path + '../../multiplesequencealign/testdata/setoxin.ref', checkIfExists: true),
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why the ../../?

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The test file comes from the multiplesequencealign branch test datasets, instead of modules. It is also used across other nf-core modules with this format. This file is better suited for the cmaple tests. Shall I maybe push this alignment file to the nf-core/test-datasets modules branch as well? Or keep like this?

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Oooh I see.
nice trick to get data from another branch

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That won't be allowed unfortunately for modules tests in the modules repo.
Could you put this file in the nf-core/test-datasets modules branch?

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Turns out that a similar file was already on the modules branch named seatoxin-ref.aln instead of setoxin-ref. So I adjusted to source that instead!

@vagkaratzas vagkaratzas requested a review from maxulysse October 16, 2025 12:48
@vagkaratzas vagkaratzas added this pull request to the merge queue Oct 17, 2025
Merged via the queue into master with commit e502606 Oct 17, 2025
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@vagkaratzas vagkaratzas deleted the cmaple branch October 17, 2025 08:48
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2 participants