HPC

Snakemake and Slurm: How to Manage Workflow with Resource Constraint on HPC

Note: This is an update to my previous post: How to Run Snakemake pipeline on HPC. In my previous post, I disucessed some tips on how to effectively manage workflow using Snakemake on an HPC system. However, I have recently noticed that Snakemake support for --cluster-config is offcially deprecated in favor of --profile. I spent most of today digging into this feature and now I’m happy to share with you my latest setup.