SNAKeMAKE: Reproducible and Scalable Bioinformatic Workflows


Quebec City, 14-15 October 2019


Institut de Biologie Intégrative et des Systèmes (IBIS)
Pavillon Charles-Eugène-Marchand
1030, Avenue de la Médecine
Room 1210 (Hydro-Québec Room)
Université Laval
Québec (Québec) G1V 0A6

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.


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

* Paradigm, syntax and basic functionalities

* Advanced features, reproducibility and deployment

COst overview

Package 1


  300 € (approx. $454.41CAD)







Suggested hotel

Hotel Universel Quebec

2300, Chemin Sainte-Foy
Québec, QC G1V 1S5


Registration deadline  10th September 2019

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.