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SNAKeMAKE: Reproducible and Scalable Bioinformatic Workflows


Berlin, 19-20 February 2019


Course Website: https://www.physalia-courses.org/courses-workshops/course41/



Registration Deadline: Friday 20th


Instructor: Dr. Johannes Köster (University of Duisburg-Essen, GER)


Course Overview

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. Thereby, its scheduling algorithm allows Snakemake to maximize workflow execution speed while not exceeding given constraints like the number of available processor cores, cluster nodes or auxilliary hardware like graphics cards.

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.

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.


TEACHING FORMAT

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 (09:30-17:30)

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

Day 2: Work with your own project (09:30-17:30)

  • Go on with the Snakemake tutorial
  • Bring your own project and implement it in Snakemake while getting advice
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