Fix bug with probeset and index mismatch when using cellranger multi with a probeset and without a pre-built index #502
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tgelafr-pfzr force-pushed the bug/375-cellranger-multi-index-mm branch from 840a5f4 to 81cf3be Compare 
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Looks generally good, just one minor thing
However, I personally can only check if the code is good from an nf-core perspective, as I have never worked with cellranger multi
| Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.4.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
…, update tests accordingly
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Nico Trummer <nictru32@gmail.com>
tgelafr-pfzr force-pushed the bug/375-cellranger-multi-index-mm branch from 8644c49 to d070f9c Compare 
| if ( params.gex_frna_probe_set && params.gex_reference_version ) { | ||
| def probeset_file = file(params.gex_frna_probe_set) | ||
| def probeset_reference = null | ||
| probeset_file.withReader { reader -> | ||
| String line | ||
| while ((line = reader.readLine()) != null) { | ||
| if (line.startsWith("#reference_genome=")) { | ||
| ref_split = line.split("=") | ||
| if (ref_split.size() > 1) { | ||
| probeset_reference = ref_split[1].trim() | ||
| } | ||
| break | ||
| } | ||
| } | ||
| } | ||
| if ( probeset_reference != params.gex_reference_version ) { | ||
| error "Parameter 'gex_reference_version' (${params.gex_reference_version}) does not match the probeset reference genome (${probeset_reference}). Please ensure the reference genome version matches the probeset file." | ||
| } | ||
| } |
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Instead of just checking that the specified gex_reference_version matches the #reference_genome in the probset, would it also work to directly obtain it from there?
That way we would save an additional parameter and it doesn't seem to be used anywhere else.
Or would you see any downsides to this approach?
4 participants
Address #375.
I chose to enforce that the user manually pass the genome version to keep some sort of front-loaded check on the reference matching the probeset.
Updated tests accordingly.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.CHANGELOG.mdis updated.