Online Snakemake workshop – Johannes Köster

Date: 13 May 2020, 09:00-17:00
Location: online via Zoom
Study load: 0.3 ECTS for a full day
Capacity: 40 participants
Target group: PhD candidates & postdocs registered with EPS; employees Genetwister Technologies; EPS staff members; MSc students affiliated with an EPS chair group
Registration fee: no costs involved
Registration: now closed

The Graduate School EPS and Genetwister Technologies are organizing a one-day online Snakemake workshop. It will be given by Dr. Johannes Köster from the University of Duisburg-Essen, the author of Snakemake.

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 150k downloads on Bioconda, Snakemake is a widely used and accepted standard for reproducible data science that has powered numerous high impact publications.

Program

09:00-09:30      Presentation: Introduction to Snakemake
09:30-12:00       Tutorial: Basic practical session
12:00-13:00       Lunch break
13:00-13:30       Presentation: Advanced usage of Snakemake
13:30-17:00       Tutorial: Advanced practical session

Requirements
Participants are expected to have basic programming skills, ideally in Python. They need to be able to install Snakemake on their own computers prior to the start of the workshop. Please check the different procedures for Linux, MacOS X and Windows here: https://snakemake.readthedocs.io/en/stable/tutorial/setup.html#setup

Registration
Registration for this workshop is now closed.