nf-core / nf-core/pathogenepidemiology
Create short read analysis track
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- Dominant language
- Nextflow
- Stars
- 3
- Forks
- 2
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 6
Description
Filtered short reads should be aligned and have variant/haplotype calling performed on them before being merged back together with the long read track
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 existing long-read track and the pipeline entry points that merge tracks. Determine how filtered short reads are represented, then identify where alignment and variant or haplotype calling belong; the work is done when the short-read results are produced and merged with the long-read track.
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
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 42/100