Dear @johanneskoester ,
I would like to be able to specify resource and threads for all my snakemeke rules, but give the users of my pipeline the possibility to modify them easily.
One option is to do this in the config file add a 'threads' and 'mem' option for each rule or groups of rules. However, I think it would be more intelligent to separate this from the workflow and use the --cluster file, where default parameters and rule-specific parameters can be chosen.
But then there are rules, where the resource attributes can be passed to the command. So I would need to read the cluster file in the snakefile.
I wonder what was your thoughts on this.
Dear @johanneskoester ,
I would like to be able to specify resource and threads for all my snakemeke rules, but give the users of my pipeline the possibility to modify them easily.
One option is to do this in the config file add a 'threads' and 'mem' option for each rule or groups of rules. However, I think it would be more intelligent to separate this from the workflow and use the
--clusterfile, where default parameters and rule-specific parameters can be chosen.But then there are rules, where the resource attributes can be passed to the command. So I would need to read the cluster file in the snakefile.
I wonder what was your thoughts on this.