This short course is meant to teach participants the automation of pipelines. For this, the snakemake workflow engine is introduced.
It will be presented how to write recipes with this engine which are independent of the programming language used. Further, the capabilities of snakemake to parallelize these workflows are demonstrated. To conclude, a custom workflow will then be submitted to the cluster to run on multiple machines.
The course will be fully interactive.
Users will work on hemera and are expected be sufficiently introduced to the slurm scheduling system.