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Fix barcode usage #543

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Fix barcode usage #543

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f1ba09b
Fix barcode usage
nictru May 12, 2026
8f18c72
Merge branch 'dev' into gex_barcodes
nictru May 12, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## Fixes

- Pass `--gex_barcode_sample_assignment` into `cellranger/multi` as the `cmo_barcode_assignment` input (previously omitted) ([#543](https://github.com/nf-core/scrnaseq/pull/543))
- Fix `modules.config` structure to make sure all ways of providing the `aligner` param work ([514](https://github.com/nf-core/scrnaseq/pull/514))
- Fix [515](https://github.com/nf-core/scrnaseq/issues/515), failure when running singleplex flex data by updating cellranger multi module ([517](https://github.com/nf-core/scrnaseq/pull/517))
- Fix [522](https://github.com/nf-core/scrnaseq/issues/522), protocol not being passed correctly when running cellranger multi ([524](https://github.com/nf-core/scrnaseq/pull/524))
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2 changes: 1 addition & 1 deletion subworkflows/local/align_cellrangermulti.nf
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Expand Up @@ -214,7 +214,7 @@ workflow CELLRANGER_MULTI_ALIGN {
ch_beam_control_panel_csv,
ch_gex_cmo_set,
ch_cmo_barcode_csv,
[],
ch_gex_barcodes,
ch_frna_sample_csv,
ch_ocm_barcode_csv,
params.skip_cellranger_renaming
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