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.
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
- follows the recommended Snakemake project structure,
- uses conda environments for integrated package management,
- uses the Slurm executor plugin to submit the workflow steps as cluster jobs,
- decouples the workflow and Slurm resource configurations using a Snakefile and a profile configuration file, respectively.