CODEWITHSUNDEEP
pythonsnakemake
newuser
newuser

Reputation: 39

Snakemake: specify cluster per rule

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?

Upvotes: 1

Views: 73

Answers (1)

SultanOrazbayev
SultanOrazbayev

Reputation: 16571

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.

Upvotes: 1

Related Questions