Snakemake and Slurm

[mweberr]

Hi all,
I need some advice to load my Snakemake pipeline onto a Slurm-managed computing resource.

1. How to add the following parameters to the profile from sbatch ?
   sbatch -p target -c 30 --mem=3G --time=12:00:00
   The Snakemake-Profiles generated config.yaml does not contain any information about partitions and memory. I presume it is the default-resources but I cannot find the relevant information in the documentation.

2. How to call Snakemake with slurm?
   Is it still necessay to call Snakemake --slurm in addition to --profile slurm ?

Thank you for all help!

[mbhall88]

1. Are you saying you want -p target -c 30 --mem=3G --time=12:00:00 to be the default for every rule in your pipeline?
2. No, you would generally use one or the other as they're kind of doing much the same thing (not quite the same though)