Containerized Workflows

Intro to workflows for efficient automated data analysis, using snakemake



> C. Titus Brown,

> Sateesh Peri,


No license; the below content is under CC0. (Do with it what you will, and I hope it’s useful!)

In this breakout session you’ll learn about snakemake, a workflow management system consisting of a text-based workflow specification language and a scalable execution environment. You will be introduced to the Snakemake workflow definition language and how to use the execution environment to scale workflows to compute servers and clusters while adapting to hardware specific constraints.

Snakemake is designed specifically for computationally intensive and/or complex data analysis pipelines. The name is a reference to the programming language Python, which forms the basis for the Snakemake syntax.


You don’t need to be an expert at Python to use Snakemake, but it can sometimes be very useful.

Click here for Snakemake setup and complete tutorial.