Abstract

Here you will learn to write both Make and Snakemake workflows. We teach two workflow engines because Snakemake uses a lot of the concepts of Make, and these concepts are somewhat complex and a very different way of thinking than you might be used to with workflow design.

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• What is Make & Snakemake
• What is a Makefile/Snakefile
• How do these improve pipelines over simple scripts?
• Why is Snakemake better for scientific research and how can I use it
• How do I use conda envs with Snakemake?

Learning Objectives

• Write a snakefile that does a simple QC and Mapping workflow