nf-core / nf-core/pairgenomealign
Add a `--circular` option
Open
Nobody has claimed this yet.
enhancement
- Dominant language
- Nextflow
- Stars
- 12
- Forks
- 5
- Avg merge
- 1d 10h
- Merged PRs (30d)
- 6
Description
Description of feature
The new LAST version has a --circular option. It is useful for searching for Nuclear mitochondrial DNA segment (NUMTs) in nuclear genomes. It would be cool to support it.
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 where the pairgenomealign workflow assembles and runs LAST commands, then trace how command-line options are exposed. The change is complete when the pipeline accepts a circular-search option and passes it through to LAST for NUMT searches; verify the relevant workflow execution with a suitable example.
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