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Add homopolish for nanopore-only assembly
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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.mdis updated. - [ ] Output Documentation in
docs/output.mdis updated. - [x]
CHANGELOG.mdis updated. - [x]
README.mdis 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