Technology-invariant pipeline for spatial omics analysis (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / ...) that scales to millions of cells
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).
Description
Snakemake doesn't correctly recognise the number of threads from the
cluster
command in the slurm config yaml. Theprovided 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 asthreads
in thedefault-resources
inside the yaml).