Snakemake is an incredibly useful workflow management tool that allows you to run pipelines in an automated way. Simply put, it allows you to define inputs and outputs for different steps that depend on each other, Snakemake will then run jobs only when the required inputs have been generated by previous steps. A previous blog post by Tobias is a good introduction to it – https://www.blopig.com/blog/2021/12/snakemake-better-workflows-with-your-code/. 

However, often pipelines are computationally intense and we would like to run them on our HPC. Snakemake allows us to do this on slurm using an extension package called snakemake-executor-plugin-slurm.