nf-core / nf-core/scdownstream
Add emptydrops for empty droplet detection
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- Dominant language
- Nextflow
- Stars
- 115
- Forks
- 66
- Avg merge
- 11d 6h
- Merged PRs (30d)
- 4
Description
Currently cellbender is the only tool available in the pipeline for empty droplet detection. nf-core/scrnaseq had emptydrops available in all versions <3.0.0, then the empty droplet detection was unified between nf-core/scrnaseq and nf-core/scdownstream through a shared subworkflow for cellbender empty droplet detection.
The old scrnaseq implementation of emptydrops can be used as a template for this purpose.
Check NBIS hackathon slides for more info
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 reviewing the linked nf-core/scrnaseq emptydrops.nf implementation and compare it with the current cellbender empty-droplet path in nf-core/scdownstream. Use the NBIS hackathon slides for context. Done means emptydrops is available in the pipeline as an alternative empty-droplet detection approach.
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
- 38/100