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implemented dynamic filtering option per #174#204

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ctastad wants to merge 1 commit intonf-core:devfrom
ChoBioLab:dynamic-filtering
Open

implemented dynamic filtering option per #174#204
ctastad wants to merge 1 commit intonf-core:devfrom
ChoBioLab:dynamic-filtering

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@ctastad ctastad commented Jul 18, 2025

PR checklist

  • 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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/scdownstream branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

Implemented MAD-based dynamic filtering option following method given in sc best practices.

https://www.sc-best-practices.org/preprocessing_visualization/quality_control.html#filtering-low-quality-cells

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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