RFE: Quality trimming in the pipeline
Open
Nobody has claimed this yet.
enhancement
- Dominant language
- Nextflow
- Stars
- 29
- Forks
- 16
- Avg merge
- 5d 36m
- Merged PRs (30d)
- 1
Description
Description of feature
While not necessarily required, these can fit some recommended protocols by vendors like KAPA, (cf. "KAPA Bioinformatics Analysis for Longitudinal Detection of Circulating Tumor DNA"), where the non-UMI sequences are trimmed using fastp.
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 tracing the pipeline's read-processing steps and identify where non-UMI sequences are handled. Review how fastp is currently invoked, if at all, and verify the finished pipeline performs the requested quality trimming for the cited workflow.
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
- 42/100