nf-core / nf-core/scdownstream
First class support for zarr input and output
Nobody has claimed this yet.
- Dominant language
- Nextflow
- Stars
- 115
- Forks
- 66
- Avg merge
- 11d 6h
- Merged PRs (30d)
- 4
Description
Description of feature
Judging by the documentation:
nf-core/scdownstream is a bioinformatics pipeline that can be used to process already quantified single-cell RNA-seq data. It takes a samplesheet and H5AD-, SingleCellExperiment/Seurat- or CSV files as input and performs quality control, integration, dimensionality reduction and clustering. It produces an integrated H5AD and SingleCellExperiment file and an extensive QC report.
the pipeline currently only mentions and/or supports h5ad but zarr is becoming increasingly used and supported at scverse. Let's ensure that the pipeline has full support.
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 pipeline documentation and the existing H5AD, SingleCellExperiment/Seurat, and CSV input and output paths. Trace where supported formats are declared and processed, then verify that Zarr works as both input and output and that the documentation describes it.
Written by the indexing model from the issue text.
Assessment
- Domain
- data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 42/100