Snakemake: Reproducible and Scalable Bioinformatic Workflows


3-4 May 2022


This course will be held online in response to the coronavirus outbreak

Course Overview

The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.

With over 260k downloads on Bioconda, Snakemake is a widely used and accepted standard for reproducible data science that has powered numerous high impact publications. With on average 6 new citations per week, it is one of the most widely used reproducibility frameworks in science.

This course will introduce the Snakemake workflow definition language and describe how to use the execution environment to scale workflows to compute servers and clusters while adapting to hardware specific constraints. Further, it will be shown how Snakemake helps to create reproducible analyses that can be adapted to new data with little effort.

Targeted audience & ASSUMED BACKGROUND

The examples presented in this course come from Bioinformatics. However, Snakemake is a general-purpose workflow management system for any discipline. We ensured that no bioinformatics knowledge is needed to understand the tutorial.

Participants are invited to bring their own data.


The workshop is delivered over 2 days (see the detailed curriculum below). The lectures are interactive with active discussion where asking questions is strongly encouraged.


# Day 1: Snakemake tutorial (2-8 PM CET)

* Paradigm, syntax and basic functionalities
* Advanced features, reproducibility and deployment

# Day 2: Work with your own project (2-8 PM CET)

* Design patterns and best practices
* Go on with the Snakemake tutorial
* Bring your own project and implement it in Snakemake while getting advice



COst overview

Package 1

350 €

Cancellation Policy:




> 30  days before the start date = 30% cancellation fee


< 30 days before the start date= No Refund.




Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.