Snakemake

Snakemake is a workflow management tool. It is used to create reproducible and scalable data processing workflows (pipelines).

Workflows are described via a human readable, Python based language.

Example project

To get started using Snakemake on Triton, we have prepared a git repo with a small example project.

You can clone the repo, follow the instructions in README.md to run the project on Triton, and use it as a starting point for your own workflow.

The project

  1. follows the recommended Snakemake project structure,

  2. uses conda environments for integrated package management,

  3. uses the Slurm executor plugin to submit the workflow steps as cluster jobs,

  4. decouples the workflow and Slurm resource configurations using a Snakefile and a profile configuration file, respectively.