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Fix #522: Protocol processing for cellrangermulti #524

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Merged
tgelafr-pfzr merged 3 commits into from
Feb 25, 2026
Merged

Fix #522: Protocol processing for cellrangermulti #524

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9973819
Properly pass protocol to cellranger multi calls
tgelafr-pfzr Feb 24, 2026
017270a
Update changelog
tgelafr-pfzr Feb 24, 2026
4847026
fix changelog hyperlink
tgelafr-pfzr Feb 24, 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

- 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))

## v4.1.0 - 2025-08-01

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1 change: 1 addition & 0 deletions workflows/scrnaseq.nf
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Expand Up @@ -227,6 +227,7 @@ workflow SCRNASEQ {
if (meta.feature_type.toString() == 'gex') {
parsed_meta.options['create-bam'] = params.save_align_intermeds // force bam creation -- param required by cellranger multi
if (meta.expected_cells) { parsed_meta.options['expected-cells'] = meta.expected_cells }
parsed_meta.options['chemistry'] = protocol_config['protocol']
}

[ parsed_meta.id , parsed_meta ]
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