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Roadie recyze extract channels #78

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@kbestak kbestak commented Feb 28, 2025

Added recyze based on legacy MCMICRO recyze with a small change that allows it to work on non-pyramidal inputs (required for test profile) as a local module.

Added test for recyze and adapted existing tests to have the additional column;

Use the following command to run pipeline with test inputs:
nextflow run . -profile test,docker --outdir <OUTDIR> --segmentation_recyze --markersheet ./assets/markers-test_roadie.csv

Output documentation would be added once the naming is agreed upon.

Closes #62

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/mcmicro 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).

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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: 3.1.1.
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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Implement Roadie for channel extraction
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