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Add parabricks-minimap2 module #8649

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@HaidYi HaidYi commented Jun 16, 2025

PR checklist

Closes #8626

  • 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

@HaidYi HaidYi self-assigned this Jun 16, 2025
@HaidYi HaidYi added new module Adding a new module gpu module uses GPU labels Jun 16, 2025
@HaidYi HaidYi mentioned this pull request Jun 16, 2025
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@HaidYi HaidYi requested a review from famosab June 16, 2025 16:12
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Looks good some minor additions and one request :)

assertAll(
{ assert process.success },
{ assert snapshot(
cram(process.out.cram[0][1]).getReadsMD5(),
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Does this work??? I thought we ususally need to hand the fasta file to get the READSMD5 for cram files 🤔

Comment on lines +12 to +13
tuple val(meta3), path(interval_file)
tuple val(meta4), path(known_sites)
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These are empty for all your tests. Can you please add tests with interval_file and known_sites? :)

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New module: Parabricks MiniMap2
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