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Workflows using Snakemake




Snakemake is a work flow tool, implemented in python, that helps you create parallel, modular work flows and run them on a SLURM cluster. In this 2-hour hands-on session we will create and run several simple work flows, examine their graphical output, and execute them on a SLURM cluster at CHPC.


To get the most from this workshop you should have the following:

  • a laptop that can connect to the campus WiFi
  • a CHPC account
  • some familiarity with the shell command line and shell scripting
  • the ability to use a text editor
  • a little familiarity with python
  • familiarity with SLURM commands for submitting jobs to a cluster


The slides are available here: workflows_with_snakemake.pdf

The exercises and solutions are located here:

To download the exercises and solutions, log in to your CHPC account on one of the frisco nodes (which are numbered 1-8, for example "") and execute the following commands:

module load git

git clone

Last Updated: 11/29/23