SNAKeMAKE: Reproducible and Scalable Bioinformatic Workflows


26-27 October 2020


Freie Universitat Berlin (Germany)

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 clean and easy to read 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.
Since its publication, Snakemake has been widely adopted and was used to build analysis workflows for a variety of high impact publications. With about 3 new citations per week, it is one of the most widely used reproducibility frameworks in science.

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.


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)

* Design patterns and best practices
* Go on with the Snakemake tutorial
* Bring your own project and implement it in Snakemake while getting advice



COst overview

Package 1

This includes course material and coffee breaks 


Package 2

This includes course material, coffee breaks, lunches and accommodation.

  350 € (VAT incl.)

630 € (VAT incl.)

Accommodation (from Sunday/check-in to Tuesday/check-out) at the *** Novum Hotel Ravenna Berlin or at Hotel Eckstein, in shared rooms (max. 2 people per room), en-suite bathroom, breakfast included.

Registration deadline  26th September 2020

Cancellation Policy:




> 30  days before the start date = 30% cancellation fee


< 30 days before the start date= No Refund.




Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.