Snakemake workshop by Johannes Köster (CWI)

On Thursday 13 September, you may join our Snakemake workshop by Johannes Köster from CWI. 
The course will contain:
– an introduction on the Snakemake workflow definition language
– a description on how to use the execution environment to scale workflows to compute servers and clusters while adapting to hardware specific constraints
– how Snakemake helps to create reproducible analyses that can be adapted to new data with little effort.

Schedule
10:00 – 17:00

Talk: Introduction
Hands-on session: basic concepts
Talk: Advanced functionality
Hands-on session: advanced functionality
(Lunch at 12:30)

Room to be announced!

Requirements
– a notebook with Linux or macOS, or Windows with a Linux virtual machine
– basic knowledge of the Python programming language

Registration
Places are limited from 20 to 30 persons, depending on the room, and are on first register first serve bases. Please register by sending an e-mail to John van Dam with your full name, institute and department.

About Snakemake
Data analyses usually entail the application of many command line tools or scripts to transform, filter, aggregate or plot data and results. With ever increasing amounts of data being collected in science, reproducible and scalable automatic workflow management becomes increasingly important. Snakemake is a workflow management system, consisting of a text-based workflow specification language and a scalable execution environment, that allows the parallelized execution of workflows on workstations, compute servers and clusters without modification of the workflow definition. Moreover, Snakemake allows to control the software stack for each step in the workflow via the Conda package manager or containers.

Since its publication, Snakemake has been widely adopted and was used to build analysis workflows for a variety of high impact publications. With about 5000 homepage visits per month, it has a large and stable user community.