I am here listing information about running Snakemake on the HPC for my pipeline spike https://github.com/sjanssen2/spike, which performs multiple steps to analyse NGS whole exome data.

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You might have to install (mini|ana)conda https://docs.conda.io/en/latest/miniconda.html, create an environment https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html#managing-environments and install snakemake https://snakemake.readthedocs.io/en/stable/getting_started/installation.html#installation-via-conda first.

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Snakemake greatly supports execution of a pipeline on a grid compute system with very little overhead. However, it will help reading Snakemake's own documentation to get familiar with with basic concepts and commands: https://snakemake.readthedocs.io/en/stable/executable.html#cluster-executionWe are here listing our best practice experience running `spike` on the `High Performance Computing` (HPC) system at University of Duesseldorf: https://www.zim.hhu.de/high-performance-computing.html Great people support users on the HPC via https://rocketchat.hhu.de/ or by phone or email and it is definitively worth reading their Wiki https://wiki.hhu.de/display/HPC/Wissenschaftliches+Hochleistungs-Rechnen+am+ZIM **before** submitting thousands of jobs to their grid.

Compose the Snakemake master command

Here, I am giving some background information about the multiple flags you should set when executing a `spike` spike pipeline via Snakemake.

Arguments

--cluster-config cluster.json

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