Snakemake on NeSI

A short tutorial on using the workflow engine Snakemake on the NeSI HPC cluster


This is an introductory tutorial for working with Snakemake on NeSI high-performance computer cluster. This tutorial assumes that you have a basic knowledge of Snakemake and Bioconda to develop your bioinformatics workflows.


Get a quick introduction to conda and Snakemake at

Here, you will learn how to configure the NeSI computing cluster and your workflow to run all jobs that your workflow needs to run with the Slurm system.

Currently, Dr. Sebastian Schmeier is teaching this material at Massey University in Auckland, New Zealand. More information about other bioinformatics material, tutorials, and our research can be found on the webpages of the Schmeier Group (


A PDF-version of this tutorial can be downloaded here.