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Snakemake-Profiles / slurm

Cookiecutter for snakemake slurm profile
MIT License
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put cluster_config in config.yaml #37

Closed jos4uke closed 4 years ago

jos4uke commented 4 years ago

Hi

I would like to ask if it is possible to create a cluster_config key in config.yaml and call it in slurm-submit.py script. It would make it more flexible to update the cluster config file path and thus the profile without touching the source. Thanks in advance Jos

mwort commented 4 years ago

Hi Jos, I think I know what you are getting at, but I think this wouldnt work for two reasons (correct me if I'm wrong): 1) the cluster_config in the profile config.yaml will only be considered if cluster_config is not parsed directly to SM. That would mean default parameters would not be considered. Stuff like env variable expansion probably would work either. 2) SM's cluster_config argument is officially deprecated since v5.10, i.e. cluster_config will soon not be accepted in the profile config.yaml.

Hope that makes sense. This is a cookiecutter template, I wouldnt be too shy changing src files;)

jos4uke commented 4 years ago

Hi Michel

sorry for the late reply You are right, I was thinking --cluster_config was deprecated with v5.10 and soon will be unavailable so it could work for later versions. And I was not aware this will be discarded from config.yaml, only considered the CLI. Thanks for enlightening me about that. Best