8000 [WIP] DSL2: Doc updates by TCLamnidis · Pull Request #1200 · nf-core/eager · GitHub
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[WIP] DSL2: Doc updates - #1200

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[WIP] DSL2: Doc updates#1200
TCLamnidis wants to merge 13 commits into
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doc_updates

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@TCLamnidis
@TCLamnidis TCLamnidis commented Nov 6, 2026 •
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This PR updates the docs to match the dev version thus far.

  • usage.md
  • output.md

Also adds running of BEDTOOLS_COVERAGE_BREADTH, which seems to have been unimplemented so far.

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
    • If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • 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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