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feat (closes #7246): add new component: leafcutter/differentialsplicing#12271

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feat (closes #7246): add new component: leafcutter/differentialsplicing#12271
JTL-lab wants to merge 3 commits into
nf-core:masterfrom
JTL-lab:leafcutter/differentialsplicing

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@JTL-lab JTL-lab commented Jul 7, 2026

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PR Description

This PR adds a new module leafcutter/differentialsplicing for running Leafcutter differential splicing analysis to determine statistically significant junction usage changes between biological conditions of interest. This module relies on the new Python reimplementation of Leafcutter (leafcutter-ds) here (also documented in the meta.yml).

PR checklist

Closes #7246

  • 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

@JTL-lab JTL-lab enabled auto-merge July 8, 2026 18:55
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new module: leafcutter/differential_splicing

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