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Add dream module #7750

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Add dream module #7750

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nschcolnicov
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@nschcolnicov nschcolnicov commented Mar 6, 2025

PR checklist

Closes nf-core/differentialabundance#363

  • 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

@atrigila
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Nico, I found several issues and errors in this original module. I've been re-writing a little bit differently. I am going to push my changes and suggestions here + the migration to the template form.

@atrigila
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@nschcolnicov feel free to check if these changes suit the pipeline structure and what you and Alan envisioned and if all looks good to you we could ask for reviewers.

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Support for linear mixed effects models via DREAM
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