e-learning
Make & Snakemake
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
Licence: Creative Commons Attribution 4.0 International
Keywords: Foundations of Data Science
Target audience: Students
Resource type: e-learning
Version: 6
Status: Active
Prerequisites:
- Advanced CLI in Galaxy
- CLI basics
Learning objectives:
- Write a snakefile that does a simple QC and Mapping workflow
Date modified: 2024-06-11
Date published: 2021-11-18
Contributors: Anthony Bretaudeau, Björn Grüning, Donny Vrins, Helena Rasche, Saskia Hiltemann
Scientific topics: Software engineering
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