e-learning

Make & Snakemake

View material

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

Authors: Avans Hogeschool, Bazante Sanders, Donny Vrins, Helena Rasche

Contributors: Avans Hogeschool, Bazante Sanders, Donny Vrins, Helena Rasche

Scientific topics: Software engineering

External resources:
Associated Training Datasets
Activity log