Deploying a variant analysis pipeline with Snakemake

Galaxy is mostly geared toward users who are less inclined to program. Knowing how to deal with it, even if you prefer a more programmer-friendly environment, is important because of its pervasiveness. It is reassuring that an API exists to interact with Galaxy. But if you want a more programmer-friendly pipeline, there are many alternatives available. In this chapter, we explore two widely used programmer-friendly pipelines: snakemake and Nextflow. In this recipe, we consider snakemake.

Snakemake is implemented in Python and shares many traits with it. That being said, its fundamental inspiration is a Makefile, the framework used by the venerable make-building system.

Here, we will develop a mini variant analysis pipeline with snakemake. The objective here is not to get the scientific part right – we cover that in other chapters – but to see how to create pipelines with snakemake. Our mini pipeline will download...