cellranger multi with gene expression and CRISPR data fails to process CRISPR data

[svigneau]

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

Running the pipeline using cellranger multi (cellrangermulti aligner option) with gene expression and CRISPR libraries (e.g., this dataset) fails to process CRISPR data (only gene expression data are processed). This could be traced to the following:

• typo in modules/nf-core/cellranger/multi/templates/cellranger_multi.py: for modality in ["gex", "vdj", "ab", "beam", "cmo", "cirspr"]: to be replaced by for modality in ["gex", "vdj", "ab", "beam", "cmo", "crispr"]:
• incomplete checks in modules/nf-core/cellranger/multi/main.nf: include_fb = ab_fastqs.first().getName() != 'fastqs' && fb_reference ? '[feature]' : '' to be replaced by include_fb = (ab_fastqs.first().getName() != 'fastqs' || crispr_fastqs.first().getName() != 'fastqs') && fb_reference ? '[feature]' : ''

I will submit a pull request with the fixes.

Command used and terminal output

Relevant files

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System information

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