nf-core / nf-core/viralintegration
Replace bamsifter with deepTools bamCoverage
Open
Nobody has claimed this yet.
enhancement
- Dominant language
- Python
- Stars
- 19
- Forks
- 11
- PR merge metrics
- No merged PRs in 30d
Description
Description of feature
bamsifter isn't in the CTAT image, and I think deepTools bamCoverage can do the same thing?
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
No file or test is named in the issue. Start by locating the pipeline step that invokes bamsifter and reviewing how its output is used, then compare it with deepTools bamCoverage. Done means the pipeline no longer depends on bamsifter and produces the intended equivalent coverage output.
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
- 35/100