I am running a large workflow in snakemake, that employs cluster execution (--cluster qsub) and a custom profile (--profile custom) for execution in a user-specific computing environment. How can I specify which computing environment (cluster, profile or local) to use for every rule?
Otherwise, would it be possible to chain multiple sub-workflows with different execution options?
Specifying rules for local execution can be done via localrules:
The keyword localrules allows to mark a rule as local, so that it is not submitted to the cluster and instead executed on the host node
See docs.
localrules: all, foo
rule all:
input: ...
rule foo:
...
rule bar:
...
AFAIK it's not possible to specify a custom profile per individual rule.