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Add pbcpgtools/alignedbamtocpgscores module #9312

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Add pbcpgtools/alignedbamtocpgscores module #9312

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@inemesb inemesb commented Oct 31, 2025

PR checklist

Closes #9277

  • 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

@inemesb inemesb marked this pull request as ready for review October 31, 2025 11:21
SPPearce
SPPearce reviewed Oct 31, 2025
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Hmm.
It looks like this tool sometimes makes one bed/index/bw file, and sometimes makes three?
Would it make sense to put them into different output channels?

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inemesb commented Nov 3, 2025

Thank you for the feedback @SPPearce! I added the extra phased files as optional output channels as you suggested, this might make the module more useful in general.

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SPPearce approved these changes Nov 3, 2025
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Great, thanks!

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@SPPearce SPPearce SPPearce approved these changes

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new module: pbcpgtools/alignedbamtocpgscores

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@inemesb @SPPearce