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Closes nf-core/differentialabundance#616

  • 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.
  • 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

@delfiterradas delfiterradas self-assigned this Jan 15, 2026
@delfiterradas delfiterradas marked this pull request as ready for review January 16, 2026 15:08
@delfiterradas delfiterradas marked this pull request as draft January 16, 2026 15:39
@delfiterradas delfiterradas marked this pull request as ready for review January 16, 2026 17:05
@delfiterradas delfiterradas requested a review from grst January 16, 2026 17:42
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I'm assuming the ext.when thing is a relic?

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Dream normalized matrix should be generated only once

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