What is Snakemake?

Snakemake is a workflow management system written in Python that is used to create reproducible and scalable data analyses. It allows users to define complex workflows using a declarative rule-based language. Each rule describes how to create specific output files from specific input files. Snakemake automatically determines the dependencies between rules and executes them in the correct order, often in parallel, to achieve the desired output. It is commonly used in bioinformatics, genomics, and other data-intensive fields to automate and manage complex analysis pipelines.