Introduction to Snakemake workflows

2024-10-15

Chloé QUIGNOT (BIOI2 @I2BC) - ORCID: 0000-0001-8504-232X

Source: adapted from FAIRbioinfo 2021 training material of the IFB and Snakemake introduction tutorial from BIOI2

Material under CC-BY-SA licence

The principle behind Snakemake

Snakemake = Python (aka “snake”, a programming language) + Make (a rule-based automation tool)

Workflows are like legos:

Workflows are made up of blocks, each block performs a specific (set of) instruction(s)

1 “block” = 1 rule:

- 1 rule = 1 instruction (ideally) - inputs and outputs are one or multiple files - at least 1 input and/or 1 output per rule

Linking data flows

Rule order is not important…

execution order ≠ code order => Snakemake does a pick & mix of the rules it needs at execution

…but matching file names is key!

Rules are linked together by Snakemake using matching filenames in their input and output directives.