I'm using snakemake to orchestrate an analysis pipeline. Some tasks are very small (e.g. create some symlinks) while others take hours. Is there a way to use --cluster for some of them but execute others just locally?
localrules does just this. When the example below is run with --cluster, bar jobs are run in cluster and foo jobs are run locally.
localrules: foo
rule foo:
...
rule bar:
...