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Add scds module #6907

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Add scds module #6907

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@cakirb cakirb commented Oct 30, 2024

This PR introduces a module for scds to address issue nf-core/scdownstream#118. Most of the code in this module is adapted from a local module in the scdownstream pipeline originally developed by @nictru (link).

While the module is functionally complete and ready for use, testing is currently impacted by a syntax issue in scds related to the xgboost version (see proposed fix: kostkalab/scds#9).

This PR should be retested once the scds package supports both older and newer xgboost versions, allowing compatibility across environments.

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

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Improve stub and version capture

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3 participants