Snakemake is a workflow management tool to perform a number of related tasks (aka "rules" in Snakemake lingo) in an efficient, reproducible and readable way. It uses a simple vocabulary to define expected input, output, parameters, script and resources for each rule. In this tutorial, we will go through the following:
- Snakemake vocabulary and syntax
- Constructing a basic workflow with 1 rule
- Various kinds of tasks (shell, R/python scripts, conda environments)
- Parameters, threads, resources
- Passing additional variables in a configuration file
- Wildcards
By the end of the tutorial, we will learn how to build a slightly more complicated workflow with multiple rules, using some of the above concepts.
Some familiarity with Python 3 & basic Conda commands is essential. (e.g. setting up and starting a Conda environment, loading python modules, python data types, working with lists, dicts and tuples) There are plenty of resources on the web for Python 3, and go here for an intro to conda.
At a minimum, you should have Conda (Miniconda is fine), and Snakemake installed. Read the Snakemake docs on how to install these.
I will use bash commands or R scripts in the tutorial, so Linux or MacOS is ideal. For the purpose of this tutorial alone, Windows Subsystem for Linux on Windows 10 should work, but may not work reliably.
I have built up the concepts step-by-step with each individual workflow. Going through them in the following order makes the most sense. Go through each of the Snakefiles below before running them, to understand Snakemake syntax. It is not important for you to know the shell commands themselves, as you can substitute them with any other task you like.
First, clone this repo (all code preceded by $ is to be entered at the terminal (command-line):
$ git clone https://github.com/sraorao/snakemake_GMS_MT2021
$ cd snakemake_GMS_MT2022