Using --cluster parameter to run jobs

[ccbaumler]

Attempted to run --cluster "sbatch -t {resources.runtime_min} -J gristing-p bmm -n 1 -N 1 -c {threads} --mem={resources.mem_mb}"

Met this error:

RuleException in rule download_sra_wc  in line 495 of /home/baumlerc/miniconda3/envs/grist/lib/python3.9/site-packages/genome_grist/conf/Snakefile:
AttributeError: 'Resources' object has no attribute 'runtime_min', when formatting the following:
sbatch -t {resources.runtime_min} -J gristing -p bmm -n 1 -N 1 -c {threads} --mem={resources.mem_mb}

A straight forward solution would be to include the resources: block and resource parameters to each rule. Could include this as an option in documentation as well. Thoughts?

Supp: https://snakemake.readthedocs.io/en/stable/executing/cli.html#cluster

[ctb]

that'd be great!

can you start up a PR? I can help define the specific parameters. any documentation/walkthrough of running things on cluster would be most welcome as well.