Open leoisl opened 2 years ago
Sorry, what is the issue here?
Issue is that the current default_mem_mb
implemented in the profile does not work. Adding default-resources
as specified in the previous post to config.yaml
can make it work, and we can also even further specify default disk_mb
and tmpdir
, which currently is not configurable in the profile. All these 3 options can be configured by the cookie-cutter and specified in config.yaml
snakemake
accepts a--default-resources
option that allows us to specify the defaultmem_mb
,disk_mb
andtmpdir
if a rule did not specify these directives. We can ask for these values in the cookie-cutter, and inconfig.yaml
they can be specified using the following format:Adding this to my
config.yaml
, and submitting this dummy job, which does not specify any of these directives:I got the following log:
Job script is:
if we instead specify
mem_mb
in the job:we get this log:
with this job script:
so it indeed works