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Pull request overview
Updates the pipeline’s output layout to group quantification results into per-assay subdirectories and exports count matrices in 10x-compatible Matrix Market format, aligning on-disk outputs with downstream single-cell tooling expectations.
Changes:
- Restructures output directories for unique/gene/transcript counts and cluster-level results.
- Adds
save_counts.Rhelper to exportSummarizedExperimentassays to*.mtx.gz+barcodes.tsv.gz/features.tsv.gzalongside the.rds. - Updates the R container to include
DropletUtilsand refreshes README output documentation.
Reviewed changes
Copilot reviewed 4 out of 5 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| README.md | Documents the new output directory layout and matrix outputs. |
| modules/bambu/transcript_discovery.nf | Writes unique/gene counts into dedicated directories and publishes them. |
| modules/bambu/EM_quant.nf | Writes EM quant outputs into structured directories and publishes them. |
| containers/r/Dockerfile | Adds bioconductor-dropletutils dependency required for matrix export. |
| bin/save_counts.R | New helper for exporting 10x-style matrices and saving per-directory .rds outputs. |
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