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Add homopolish for nanopore-only assembly

Open Gilbaja opened this issue 7 months ago • 0 comments
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PR checklist

  • [x] This comment contains a description of changes (with reason).
  • [ ] If you've fixed a bug or added code that should be tested, add tests!
  • [x] 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/bacass branch on the nf-core/test-datasets repository.
  • [x] Make sure your code lints (nf-core pipelines lint).
  • [x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • [x] 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.
  • [x] CHANGELOG.md is updated.
  • [x] README.md is updated (including new tool citations and authors/contributors).

Issue #66

Adds homopolish as a tool for polishing after polished by medaka.
Before executing homopolish it needs a bacteria sketch to be downloaded (3.3GB) and unzipped.
To do so, an additional module is created, and the workflow includes a condition for checking if it has been already downloaded in the output folder. It also includes a new parameter for forcing the download.

Test cmd

nextflow run . -profile test_long,conda --polish_method medaka_homopolish --outdir results

Pending tasks

  • Adding tests
  • Check with singularity

Gilbaja avatar Mar 26 '25 17:03 Gilbaja