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BBsplit unmapped - enhancement #9627

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BBsplit unmapped - enhancement #9627

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@EladH1 EladH1 commented Jan 8, 2026 •
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PR checklist

Closes #XXX

  • This comment contains a description of changes (with reason).

As this is in some cases the first alignment it's beneficial to have also unaligned fastq saved.

  • 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.
  • Broadcast software version numbers to topic: versions - See version_topics
  • 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

@EladH1 EladH1 requested a review from pinin4fjords January 8, 2026 10:09
mashehu
mashehu reviewed Jan 23, 2026
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modules/nf-core/bbmap/bbsplit/main.nf
output:
path "bbsplit_index" , optional:true, emit: index
tuple val(meta), path('*primary*fastq.gz'), optional:true, emit: primary_fastq
tuple val(meta), path('*unmapped*fastq.gz'), optional:true, emit: unmapped_fastq
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@mashehu mashehu Jan 23, 2026

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You should also add a snapshot for these in the tests/main.nf.test file

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@EladH1 EladH1 Jan 27, 2026

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thanks @mashehu I'll . do you know a bout any change in meta - I don't manage to --fix it for linting

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@pinin4fjords pinin4fjords Awaiting requested review from pinin4fjords pinin4fjords is a code owner

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