Supporting multiple taxons with tax2filter
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- Dominant language
- Nextflow
- Stars
- 24
- Forks
- 10
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Description
Description of feature
The current version of tax2filter only allows the filtering out of a single taxon. However, it would be more useful if it could support multiple taxons separated by either a comma or semicolon. In my metagenomics project, I need to filter out human, bacteria, and archaea. Unfortunately, the current version of detaxizer does not permit filtering out all three taxons in one pipeline run.
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 by locating the tax2filter entry point in the detaxizer pipeline and trace how its single taxon input reaches the filtering step. Check how comma- and semicolon-separated taxons should be handled, then validate a pipeline run that filters human, bacteria, and archaea together.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100