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Fix dream to accept spaces in variable names#11077

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delfiterradas wants to merge 3 commits intonf-core:masterfrom
delfiterradas:dream_makecontrasts
Open

Fix dream to accept spaces in variable names#11077
delfiterradas wants to merge 3 commits intonf-core:masterfrom
delfiterradas:dream_makecontrasts

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PR checklist

Closes nf-core/differentialabundance#677

  • Accept spaces in variable names
  • Migrate to topic channels

  • 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 Mar 27, 2026
@delfiterradas delfiterradas marked this pull request as ready for review March 27, 2026 17:41
@delfiterradas delfiterradas requested review from atrigila and grst March 27, 2026 17:41
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variancepartition/dream makeContrasts cannot deal with spaces in variable names

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