Add support for generating mmseqs taxonomy reports
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- Dominant language
- Nextflow
- Stars
- 119
- Forks
- 40
- Avg merge
- 2d 17h
- Merged PRs (30d)
- 5
Description
Description of feature
Mmseqs has built-in support for generating some useful reports via the mmseqs taxonomyreport command. This is described in the official wiki:
https://github.com/soedinglab/mmseqs2/wiki#taxonomy-report-in-kraken-or-krona-style
It would be great to have this functionally enabled in nf-core/funcscan. It would require the creation of an additional nf-core module called MMSEQS_TAXONOMYREPORT.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the official Mmseqs taxonomyreport documentation linked in the issue, then inspect how nf-core modules are organized in funcscan. Add the MMSEQS_TAXONOMYREPORT module and connect it to the workflow so taxonomy reports can be generated; done means the feature is enabled and the relevant workflow checks pass.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100