Fix #522: Protocol processing for cellrangermulti

[tgelafr-pfzr]

Previously, the protocol parameter was not being passed to the cellranger multi call, so the value was always treated as auto. I pass it correctly.

PR checklist

• This comment contains a description of changes (with reason).
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• CHANGELOG.md is updated.

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[Copilot]

Pull request overview

This pull request fixes issue #522 where the protocol/chemistry parameter was not being passed to cellranger multi. The fix adds the protocol configuration to the GEX options metadata, following the same pattern used by the non-multi cellranger aligner.

Changes:

• Add protocol/chemistry configuration to cellrangermulti GEX options
• Update CHANGELOG to document the fix

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
workflows/scrnaseq.nf	Adds chemistry option from protocol_config['protocol'] to the GEX metadata options for cellrangermulti
CHANGELOG.md	Documents the fix for issue #522 in the changelog

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[fmalmeida]

Changes look really clean, so would be fine.
Just want to know why is needed. In cellranger multi the chemistry meta is what is used for processing?

[tgelafr-pfzr]

Changes look really clean, so would be fine. Just want to know why is needed. In cellranger multi the chemistry meta is what is used for processing?

Typically defaults to auto-detection of the chemistry based on barcodes, but you can manually specify in the cellranger call: https://www.10xgenomics.com/support/software/cell-ranger/latest/advanced/cr-multi-config-csv-opts#chem-opts

Just came up for my team with some (very) low quality data for which the barcodes were difficult to resolve. A rare use case but this will allow a better mirroring of the cellranger functionality.

[fmalmeida]

So it needs to be conditionally put as well no?

So by default keeps the auto detection but in case it is manually given then it adds?

Or this config protocol variable already works conditionally like that?

[tgelafr-pfzr]

If it's set to "auto" (which is the default for both cellranger and this pipeline), it still auto-detects the chemistry, same as if it were excluded. So I think it's fine to always set it. This mirrors the behavior for the CELLRANGER_COUNT setup: https://github.com/nf-core/scrnaseq/blob/f7bf36d7c7e4bddc5302c3facd8d19ca83e22226/subworkflows/local/align_cellranger.nf#L38C1-L39C1.