I am wondering what is the best way to combine Snakemake profiles with drmaa.
As the --cluster-config option is deprecated in favor of --profile, one would need to set cluster specific configurations via profiles also for drmaa.
If a profile sets the --cluster option, a command, possibly a Python script, can be added to the profile which collects all the cluster configuration information and is used by Snakemake to submit the jobs. However, when supplying the --drmaa option, no such command can be passed, as Snakemake uses the API to submit jobs.
Thus, to add a rule specific cluster configuration one would again need --cluster-config, which is deprecated.
Another option would be to write a cluster-submission command supplied via --cluster that uses drmaa. But I am wondering, whether that is the intended way to go?
I am wondering what is the best way to combine Snakemake profiles with drmaa.
As the --cluster-config option is deprecated in favor of --profile, one would need to set cluster specific configurations via profiles also for drmaa.
If a profile sets the --cluster option, a command, possibly a Python script, can be added to the profile which collects all the cluster configuration information and is used by Snakemake to submit the jobs. However, when supplying the --drmaa option, no such command can be passed, as Snakemake uses the API to submit jobs.
Thus, to add a rule specific cluster configuration one would again need --cluster-config, which is deprecated.
Another option would be to write a cluster-submission command supplied via --cluster that uses drmaa. But I am wondering, whether that is the intended way to go?