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BBsplit unmapped - enhancement #9627

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EladH1 wants to merge 17 commits intonf-core:masterfrom
EladH1:bbsplit_unmap
Draft

BBsplit unmapped - enhancement #9627
EladH1 wants to merge 17 commits intonf-core:masterfrom
EladH1:bbsplit_unmap

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@EladH1 EladH1 commented Jan 8, 2026

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
Comment thread modules/nf-core/bbmap/bbsplit/main.nf
Comment thread subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/meta.yml Outdated
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EladH1 commented Feb 5, 2026

The issue was not resolved as unmapped output non-deterministic result.
so every --update-snapshot generate new md5sum.

@EladH1 EladH1 marked this pull request as draft February 5, 2026 13:05
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2 participants