Burkhard Linke, Lukas Jelonek, Patrick Blumenkamp, Raphael Müller, Marius Dieckmann, Patrick Barth (BiGi)

08.10.2018 – 10.10.2018

Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, Room 0024a

Course participation:
limited to max. 20 participants
closing date for applications: 01.10.2018

This 3-day workshop covers the usage of workflow management systems for the analysis of next-generation sequence data (NGS) in the de.NBI cloud. It introduces the three workflow management systems CWL, Nextflow, and Snakemake and their ability to create shareable, reproducible, and scalable workflows. During this workshop, the participants will implement and execute workflows, and finally scale them out from single machines to the de.NBI cloud.
On all three days, the program includes extensive hands-on training to allow participants to become familiar with the presented software.

The agenda is available here.

Learning goals:
Participants will get familiar with the presented workflow management systems and the de.NBI cloud. Participants will be able to create reusable workflows and execute them in different environments.

- practical experience with Linux, Unix or derivatives
- practical experience with command line tool usage
- experience with a scripting or programming language (Python, Groovy or Java)

CWL, Nextflow, Snakemake, de.NBI cloud, Docker, high-throuhput data analyses, scalabilty

Nextflow, Snakemake, Openstack, Docker, CWL, bioconda

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