I am an avid user of Snakemake. Recently we have been refreshing our pipelines and I saw that a cluster.json file is no longer the recommended way to store the cluster configuration.
I used to start my pipelines like this:
snakemake --cluster-config cluster.json --cluster "qsub -W umask=002 -d cluster_outputs -l nodes={cluster.nodes}:ppn={cluster.ppn} -N {rule}" --jobs 245 --use-conda --rerun-incomplete --keep-going --latency-wait 60
With the cluster.json looking like this:
{
"__default__" :
{
"cluster" : "qsub",
"jobs" : 70 ,
"nodes" : 1,
"ppn" : 1
},
"rsem_quantify" :
{
"ppn" : 8
},
"star_map_human" :
{
"ppn" : 4
},
}
Now, I understand that some of this goes in to the new profiles.yaml like this:
cluster: qsub
jobs: 70
But how do I set the ppn values per rule? And how do I set the other configuration options into profile.yaml (like: snakemake "qsub -W umask=002 -d cluster_outputs -l nodes={cluster.nodes}:ppn={cluster.ppn} -N {rule}", etc.)
Any examples are appreciated, https://github.com/snakemake-profiles is not really helping