Default memory request overridden in Snakefile?
I have a Snakefile with multiple rules, and only a few need more than 1 GB / core to run on a cluster. The directive resources
works great for this, but I can't find a way to set the default. I would rather not write resources: mem_per_cpu = 1024
for every rule that doesn't require more than the default.
I understand that I can get what I want by using __default__
in the cluster config file and overriding the value mem_per_cpu
for specific rules. I hesitate to do this because the memory requirements are platform independent, so I would prefer to include them in the Snakefile itself. It would also prevent me from specifying local resource limits using a command line parameter --resources
.
Is there a simple solution with Snakemake to help me here? Thank!
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