Running on clusters

There is a file in the templates called cluster.yaml. This can be used to modify ressources needed for your data. I generally recommand moving the file to the root of the folder so that it doesn't get replaced by updates.

Bellow is an example of running on a cluster using the template file cluster.yaml on SLURM.

snakemake --cluster 'sbatch -n {cluster.n}  -t {cluster.time} --clusters=CLUSTERNAME --output={cluster.output}' --jobs N --cluster-config cluster.yaml --use-conda --local-cores C

• N: is the number of jobs you are allowed to run at the same time
• C: is the local-cores of the host machine. A few simple rules are gonna be run locally (not sent to nodes) because they are not that heavy (mostly plotting)
• CLUSTERNAME: the name of the cluster you want to use

Note: The default path for cluster logs in the cluster.yaml is logs/cluster/. If that folder doesn't exist, our cluster can't write and will crash without an error message.