I am using a profile to submit the longer jobs of my workflow to a cluster. Sometimes however I want to test something and want to run a single rule locally. Currently I have to set localrule: True when I want to do this, but this seems like an ugly workaround, since this changes the code of the rule, which I would like to avoid. Another workaround I am aware of is to supply a second profile. This doesn't seem to be a nice solution either, since that would mean maintaining two profiles, even though a single one is able to control the behaviour of both local and submission jobs. In essence I would like something like: snakemake target_file --local that overrides the local/submit behaviour just for this one call to snakemake. Is there something like this, or is this just not implemented? Continue reading...
