nf-core / nf-core/phageannotator
Add propagate to nf-core/phageannotator to identify active prophage
Open
Nobody has claimed this yet.
- #107 by @CarsonJM — closed without merging
enhancement
- Dominant language
- Nextflow
- Stars
- 19
- Forks
- 8
- PR merge metrics
- No merged PRs in 30d
Description
Add propagate (https://github.com/AnantharamanLab/PropagAtE) module to workflow to predict integrated prophage activitiy
### Tasks
- [ ] https://github.com/nf-core/phageannotator/issues/57
- [ ] https://github.com/nf-core/phageannotator/issues/58
- [ ] https://github.com/nf-core/phageannotator/issues/59
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 reading the PropagAtE project linked in the issue and the three task issues, #57, #58, and #59. Inspect the phageannotator workflow entry points to determine how the module should be integrated. Done means the workflow includes PropagAtE and can predict integrated prophage activity.
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
- 25/100