DKTK Snakemake Tutorial 2024

Learn how to do modern reproducible data science with Snakemake.

OrganizerDavid Lähnemann, bioinformatician DKTK Essen/Düsseldorf & Johannes Köster, lead developer Snakemake, founder Bioconda.
Dates2024, Mar 05 - Mar 07 (you can register for days individually)
AudiencePrimarily members of DKTK, but remaining places for any other members of the University of Duisburg-Essen and the University Medicine Essen.
LocationAudimax-Gebäude, Universitätsklinikum Essen, Kurssaal Audimax

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. Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment. Finally, Snakemake can be used to automatically generate rich interactive visual reports that contain results together data provenance information. These reports can be easily shared with collaborators (e.g. via email) and only require a web browser for viewing.

With over 800k downloads on Bioconda and on average more than 10 new citations per week in 2022, Snakemake is a widely used and accepted standard for reproducible data science that has powered numerous high impact publications.


Lunch breaks are planned for noon to 1pm. Coffee breaks will be scheduled flexibly during the course, as most parts are self-paced.

Tue, Mar 05, 9:00 am - 04:00 pmIntroduction to the linux command line (everybody) and setup of DKFZ compute cluster access (DKTK members).
Wed, Mar 06, 09:00 am - 05:00 pmSnakemake tutorial (basic usage in the morning, advanced usage in the afternoon)
Thu, Mar 07, 09:00 am - 04:00 pmSnakemake hackathon: use or create Snakemake analysis workflows


Further optional setup

Course materials

Reference materials

Registration is now closed as the course is fully booked. Thanks a lot for your interest! We will organize more courses in the future!