snakemake icon indicating copy to clipboard operation
snakemake copied to clipboard

Clarification on --default-resources input type

Open gibsramen opened this issue 2 years ago • 0 comments

Snakemake version: 7.3.0

The help for --default-resources states that arguments should be of the form NAME=INT (name=integer).

https://github.com/snakemake/snakemake/blob/cc6c9986271738dfa8394fc45720a4d756af9d0a/snakemake/init.py#L1201-L1217

However, to me it seems that Snakemake is perfectly happy taking a string as a resource. I am using the following profile and from what I can tell the fact that I pass partition=long works as intended.

cluster: "sbatch --nodes={resources.nodes} --time={resources.runtime} --cpus-per-task={resources.cpus} --mem={resources.mem_mb} --output=slurm_out/{rule}.log --partition={resources.partition}"
use-conda: True
jobs: 10
latency-wait: 60
default-resources: [cpus=4, mem_mb=8000, runtime=60, nodes=1, partition=long]

Am I misunderstanding this argument structure? If not, I think it would be useful to change the help message to reflect this.

gibsramen avatar Jun 08 '22 18:06 gibsramen