Snakemake: Reproducible science made fun and easy.

Snakemake is a language for creating scientific workflows. The name Snakemake comes from the two things it combines: the programming language Python and the automation tool Make. Python is easy to write and has a wealth of useful libraries. Make is the tool for reproducible pipelines. Mix them together and you get Snakemake, the most fun and easy way to write reproducible scientific pipelines.

Snakemake includes a wealth of features, among them:

• easy interoperability with the statistical programming language R and its libraries
• parallel and/or cluster execution for free (i.e. without having to write any additional code)
• the ability to combine premade modules to create a pipeline, Lego-style

Snakemake is already much used for writing scientific pipelines. The aim of this book is to take you from a complete novice to an advanced Snakemake hacker.