Introduction to Snakemake

Last updated on 2023-08-02 | Edit this page



  • What are Snakemake rules?
  • Why do Snakemake rules not always run?


  • Write a single-rule Snakefile and execute it with Snakemake
  • Predict whether the rule will run or not


Snakemake is a workflow tool. It takes as input a description of the work that you would like the computer to do, and when run, does the work that you have asked for.

The description of the work takes the form of a series of rules, written in a special format into a Snakefile. Rules have outputs, and the Snakefile and generated output files make up the system state.

Write a Snakemake rule file

Open your favorite editor, do the thing.

Run Snakemake

Throw the switch!


Remove the output file, and run Snakemake. Then run it again. Edit the output file, and run it a third time. For which of these invocations does Snakemake do non-trivial work?

The rule does not get executed the second time. The Snakemake infrastructure is stateful, and knows that the required outputs are up to date.

The rule also does not get executed the third time. The output is not the output from the rule, but the Snakemake infrastructure doesn’t know that, it only checks the file time-stamp. Editing Snakemake-manipulated files can get you into an inconsistent state.

Key Points

  • Snakemake is an indirect way of running executables
  • Snakemake has a notion of system state, and can be fooled.