Workflow

How to run snakemake pipeline on HPC

Why use Snakemake on HPC Snakemake is a handy workflow manager written in Python. It handles workflow based on predefined job dependencies. One of the great features of Snakemake is that it can manage a workflow on both a standalone computer, or a clustered HPC system. HPC, or “cluster” as it’s often referred to, requires additional considerations. On HPC, all computing jobs should be submitted to “compute nodes” through a workload manager (for example, Slurm).