nf-core / nf-core/scdownstream
Remove duplicate execution of Cellbender
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- Nextflow
- Stars
- 115
- Forks
- 66
- Avg merge
- 11d 6h
- Merged PRs (30d)
- 4
Description
Description of feature
Currently, cellbender is used to remove empty droplets from the input anndata. This run of cellbender also produces a filtered anndata file with ambient rna removed.
However, if you set cellbender as the method to remove ambient rna, it gets run again from scratch. The two runs are not identical, as the second run bases the priors on the first run, but I feel that this is quite redundant and perhaps the result from the first run is sufficient for empty droplet removal, as well as ambient rna filtering.
I might be missing something that happens in the background, but I think that this might just be wasting resources.
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
Trace the pipeline entry points that invoke CellBender for empty-droplet removal and ambient-RNA filtering, then compare the outputs and parameters from both runs. Determine whether one run can provide both required results, and consider the work complete when the redundant execution is removed without changing the expected filtered AnnData outputs.
Written by the indexing model from the issue text.
Assessment
- Domain
- data, machine-learning
- Issue type
- Refactor
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100