Snakemake for Lattice Quantum Field Theory

Being able to reliably run a range of tools, across multiple inputs, and in the right order, is a very common problem in computing, including in scientific data analysis. If you develop scripts for data analysis from scratch, you will usually end up running up against these challenges. Rather than reinventing the wheel,we can lean on existing tools to do this for us, letting us focus on the aspects unique to our own work. Such tools are called workflow managers.

In this lesson, we introduce Snakemake, a workflow manager originally developed for bioinformatics applications, but that maps well onto the needs of data analysis in lattice quantum field theory.

By defining rules, each of which specify how to translate one or more input files into one or more output files, we can build up a workflow that takes our raw data as input, and produces plots, tables, and other definitions that we can include in our publications.