There are a lot of snakemake tutorials out there to get you started:
- Intro to workflows for efficient automated data analysis, using snakemake This is a great introductory tutorial by Titus Brown at UC Davis
- GGG 298, Jan 2020 – Week 4 – snakemake for running workflows! is also by Titus and is a terrific intro too.
- Creating workflows with snakemake and conda on biostars is a great introduction
- A lot of anvi’o is built on snakemake, but this tutorial doesn’t really focus on the snakemake part of things.
- If you are still lost, check out twitter for a bunch of really great snakemake tutorials about all kinds of data (scRNA, nanopore, illumina, pacbio etc etc etc)
This tutorial is not one of those! It is quick, hands-on, and we’ll jump right in with little explanation (OK, there will be some). But I encourage you to read those tutorials, especially Titus’s tutorials as you will learn a lot from them.Continue reading