Snakemake

What is Snakemake?

The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition.

• To learn more about Snakemake, visit the Snakemake homepage!

• To get an impression of the Snakemake architecture, read the Snakemake paper

• To learn how to use Snakemake workflows, read the documentation.

Create your own workflows

The best starting point to create your own workflows is the Snakemake workflow template.

The template comes with a pre-configured structure that is compatible with the Snakemake catalog ‘standardized usage’. Just fork or clone the template, start addiong rules and push your workflow to Github. The structure of ‘standardized’ workflows is like this:

├── config/
│   └── config.yaml
│   └── README.md
├── workflow/
│   ├── Snakefile
│   ├── rules/
│   ├── scripts/
│   └── envs/
├── .snakemake-workflow-catalog.yml
└── README.md

Note

The template is currently not fully functional as it contains no actual Snakefile and test cases. This will be changed in the near future.