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Cellranger multi fails without --fb_reference even if not needed #409

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fmalmeida opened this issue Dec 16, 2024 · 0 comments · May be fixed by #410
Open

Cellranger multi fails without --fb_reference even if not needed #409

fmalmeida opened this issue Dec 16, 2024 · 0 comments · May be fixed by #410
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fmalmeida commented Dec 16, 2024

Description of the bug

Currently the cellranger multi subworkflow has the following snippet:

ab: meta.feature_type == "ab"
                    if (params.fb_reference){
                        return [ meta, fastq ]
                    } else {
                        error ("Antibody reference was not specified. Please provide a reference file for feature barcoding (e.g. antibody measurements).\nPlease refer to https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/inputs/cr-feature-ref-csv for more details.")
                    }

The problem is that, when ab files are not using, this reference file should not be enforced. Thus, if not passing the params.fb_reference the pipeline will fail.

We should should check if ab is used.

Proposed solution is:

ab: meta.feature_type == "ab"
                    if ((fastq.getName() == 'EMPTY') || params.fb_reference) { // Or something like that
                        return [ meta, fastq ]
                    } else {
                        error ("Antibody reference was not specified. Please provide a reference file for feature barcoding (e.g. antibody measurements).\nPlease refer to https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/inputs/cr-feature-ref-csv for more details.")
                    }

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@fmalmeida fmalmeida added the bug Something isn't working label Dec 16, 2024
@fmalmeida fmalmeida self-assigned this Dec 16, 2024
@fmalmeida fmalmeida linked a pull request Dec 16, 2024 that will close this issue
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