I am trying to run Snakemake on a SLURM cluster where accounts take the form account:subaccount
. However, when I try to write the cluster config.yaml
as follows,
executor: local
default-resources:
slurm_account: account:subaccount
slurm_partition: partition
runtime: 120 # Walltime in minutes
mem_mb: 10000
Snakemake crashes with the error
Error:
WorkflowError:
Failed to evaluate default resources value 'account:subaccount'.
String arguments may need additional quoting. Ex: --default-resources "tmpdir='/home/user/tmp'".
SyntaxError: invalid syntax (<string>, line 1)
Wildcards:
I have tried surrounding the account:subaccount
string in any number of quotation mark combinations. What I found was that passing
executor: local
default-resources:
slurm_account: "'account:subaccount'"
slurm_partition: partition
runtime: 120 # Walltime in minutes
mem_mb: 10000
seems to work for the main Snakemake routine, but then the child jobs crash with the above error.
Is there a way for me to correctly pass the SLURM account name with the colon in it to Snakemake?