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@d4straub d4straub commented Oct 7, 2025

Attempt to add COMEBin. Follows #874.

Thats a draft because there are too many issues still!
Current issues:

  • doesnt run with any test dataset
  • havent tested larger datasets yet
  • the module attempts to write into the work dir of the previous run, so I modified the nf-core module but the change is (1) inefficient and (2) will make linting fail with changed nf-core module
  • essentially it didnt run through once yet...
  • documentation is missing (citation, output)
  • GPU label might be beneficial

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/mag 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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