Update to cellranger v10.0.0 #508
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Pull Request Overview
This PR updates the cellranger tool from version 9.0.1 to 10.0.0, addressing changes in the output structure for multiplexed experiments. The key change handles an edge case where cellranger v10.0.0 now produces both raw and filtered matrices for samples and pools, which previously caused file collisions when a pool and sample are identical.
Key Changes
- Updated cellranger container from 9.0.1 to 10.0.0 across all modules (count, multi, mkgtf, mkref, mkvdjref)
- Added filtering logic in
align_cellrangermulti.nfto exclude duplicate files when demultiplexed sample ID matches the pool ID - Updated test snapshots to reflect new checksums from cellranger v10.0.0 output and adjusted test expectations for BAM file handling
Reviewed Changes
Copilot reviewed 18 out of 19 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| subworkflows/local/align_cellrangermulti.nf | Added logic to filter out duplicate matrix files when pool and sample IDs match, preventing file collisions |
| modules/nf-core/cellranger/*/main.nf | Updated container versions from 9.0.1 to 10.0.0 for all cellranger modules |
| modules/nf-core/cellranger/*/meta.yml | Reformatted YAML structure and added ontology metadata for better standardization |
| modules/nf-core/cellranger//tests/.snap | Updated test snapshots with new checksums reflecting cellranger v10.0.0 output changes |
| modules/nf-core/cellranger/count/tests/main.nf.test | Modified test to handle BAM files with unstable checksums by verifying SAM lines instead |
| modules.json | Updated git SHA references for all cellranger modules to the latest version |
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3 participants
Update to cellranger v10.0.0
They changed the output structure which necessitated a tweak in the code. For multiplexed experiments, the old output included raw matrices for the pools and filtered matrices for the samples. They are now producing both raw and filtered matrices for both the samples and pools. In the edge case where demultiplexing still happens but the pool and the sample are one and the same (e.g. some samples are being demultiplexed and others aren't in cellranger multi), this resulted in duplicate filtered and raw files for the same sample (once as a pool and once as a "sample"), producing file collisions.
To fix this, I just exclude these "duplicate" files from the output channel.
Snapshots are updated reflecting the change in output structure, differences in the matrix files, and these additional filtered/raw matrix files for samples/pools.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).CHANGELOG.mdis updated.