[Bug] Mistake in slurm config yaml

gustaveroussy / sopa

Technology-invariant pipeline for spatial omics analysis (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / ...) that scales to millions of cells

https://gustaveroussy.github.io/sopa/

BSD 3-Clause "New" or "Revised" License

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[Bug] Mistake in slurm config yaml #141

Open wlason opened 1 day ago

wlason commented 1 day ago

Description

Snakemake doesn't correctly recognise the number of threads from the cluster command in the slurm config yaml. The provided cores shows as 1.

https://github.com/gustaveroussy/sopa/blob/f1f5a99ee7f5a9489e511241a3a62bb520ec9860/workflow/slurm/config.yaml#L4

This should instead be {resources.threads}, which I tested works as expected (is set to whatever is set as threads in the default-resources inside the yaml).

quentinblampey commented 10 hours ago

Thanks @wlason for reporting this, I'm surprised I have not caught it before! I'll now have a look at your PR!