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.

Snakemake is a versatile pipeline manager for doing a lot of bioinformatics analysis, but handling wildcards in snakemake is not transparent, and here are some tips and tricks that we have gathered to help you process lots of files easily.

A very simple post about setting up reverse SSH tunneling. This is how to get to a machine that maybe behind a firewall, when you are not behind the firewall (though you need to be to set it up!)