02/07/2017 - 04/07/2017

EMBL Heidelberg
Meyerhofstraße 1
Heidelberg, Germany

Workflow Management with CWL: Bring Your Own Workflow

Code: 2017-cwl
Price: free
Location: ATC Courtyard Seminar Rooms, EMBL Heidelberg
Available seats: 40


Want to learn how to make your data analysis workflows more portable and interoperable with the Common Workflow Language (CWL*)

* “CWL is a specification for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high-performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry. CWL is developed by an informal, multi-vendor working group consisting of organizations and individuals aiming to enable scientists to share data analysis workflows. The CWL project is on Github and we follow the principles for collaborative open standards development.” (Source).

Workshop Synopsis

This hands-on workshop will provide an opportunity for participants to become familiar with analysis pipeline deployment with CWL, and to develop a CWL implementation for their own workflow.

The workshop will be hosted by EMBL Heidelberg and co-sponsored by HD-HuB, ELIXIR, and BioExcel.

Learning Goals

Interested participants (preferably in teams of two or more) are invited to bring an existing workflow (or a tested portion of a workflow in development) to a two-day hands-on workshop. There they will learn through a combination of mini-lectures and hands-on work the current best practice in how using the CWL standards to describe command line tools and the workflows made from them enables easy cross-site collaboration, portability between different computer infrastructures, and future proofing. Also welcome are data analysis tool authors who want to provide 1st class idiomatic CWL descriptions for use by their users.


  • One or more data analysis workflows consisting of command line (Linux) programs
  • and/or a tested portion of a workflow in development
  • and/or a command line data analysis tool that you are the author or maintainer for
  • A laptop running Linux or OS X with Python 2.7, Docker, and the reference implementation of CWL installed inside a virtualenv.
  • Read through and completed all exercises in the Gentle Introduction to the Common Workflow Language

Course venue

ATC courtyard training room, EMBL, Heidelberg

Course duration

July 3-4, 9:30 AM – 05:00 PM


Georg Zeller (

Malvika Sharan (

Toby Hodges (

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