update output structure#35
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Pull request overview
This PR updates the pipeline’s output layout to group count outputs into dedicated subdirectories and adds 10x-style matrix exports alongside the existing RDS artifacts.
Changes:
- Restructures transcript discovery outputs into
unique_counts/andgene_counts/directories. - Restructures EM quantification outputs into
transcript_counts_*/gene_counts_clusters/directories. - Adds the
DropletUtilsBioconductor dependency to support writing 10x-formatted outputs.
Reviewed changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 4 comments.
| File | Description |
|---|---|
| README.md | Documents the new output directory structure and adds descriptions for 10x matrix files. |
| modules/bambu/transcript_discovery.nf | Writes unique/gene counts into subdirectories and publishes those directories. |
| modules/bambu/EM_quant.nf | Writes EM outputs into subdirectories and publishes those directories. |
| containers/r/Dockerfile | Adds bioconductor-dropletutils to the R container image. |
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