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nf-core / scrnaseq

A single-cell RNAseq pipeline for 10X genomics data
https://nf-co.re/scrnaseq
MIT License
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Cellranger mkref resource flags incorrect #329

Open RPSeaman opened 1 month ago

RPSeaman commented 1 month ago

Description of the bug

Hey all, I am looking at the cellranger mkref module and noticed that automatic available resources detection has been added, but I think I have spotted an inconsistency in the flags used for memory and cores:

In their docs (https://www.10xgenomics.com/support/software/cell-ranger/latest/resources/cr-command-line-arguments) they specify --memgb and --nthreads as the two flags for cpu and memory, not --localmem and --localcores as specified in the module.

Screenshot 2024-05-13 at 3 33 42 PM

Let me know you further clarification is needed.

Command used and terminal output

No response

Relevant files

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System information

nf-core/scrnaseq 2.6.0

grst commented 1 month ago

--localmem and --localcore are global options passed to the martian runtime (martian is actually a workflow manager similar to nextflow). They should apply to all cellranger tools that are based on martian and mkref was changed from a simple script to the martian runtime in the last release.

https://www.10xgenomics.com/support/software/cell-ranger/latest/resources/cr-command-line-arguments

However, given the documentation you point at I'm wondering if we should additionally pass --nthreads because otherwise star index generation likely only runs on a single core which takes forever.

If you could update the module on nf-core/modules that would be fantastic!