Introduction to CWL and Docker

automating workflows in Life Sciences


Reproducible research is an important part of good scientific practice. Establishing robust computational analysis workflow facilitates reproducible research. There has been a strong emphasis on establishing graphic workflow management systems, such as Galaxy and Knime. However, the landscape and complexity of Linux command line tools for workflow management is vast and complicated. We aim to take advantage of European/International leaders in the field to present current scientific workflow paradigms and a lead workshops to implement a basic workflow. Topics covered include workflows and containerization.

Learning objectives



Audience and requirements

This introductory tutorial is aimed towards bioinformaticians (graduate students and researchers), who are interested in becoming familiar to Docker based workflows in CWL, as is currently supported by the ΕLIXIR-Greece Compute Infrastructure (HYPATIA).


Given that the workshop will offer hands-on training, participants will need to bring their own laptop with them.

SARS-CoV-2 guidelines

Please note that the venue requires that visitors follow the EU Digital COVID Certificate scheme as of the event date. Additional logistical details to help you plan your trip can be found on the event website. Please do not hesitate to get in touch with us if you need further assistance.

Maximum number of participants: 15 (will also have live streaming).


Date of the workshop: Monday, October 25th 2021

Please register to the workshop using this form.

Deadline: Wed 20/10/2021 12:00 local time

Notifications: Fri 22/10/2021

language of conduct: Greek



Time Details
10:00 - 10:30 Tutorial introduction
Part I: Containers Background  
10:30 - 11:30 Introduction to Containerization, run a container
Part II: Building a Container  
11:45 - 13:15 Building a container, distribute online
Part III: Basics of Workflow Languages - CWL  
14:00 - 15:30 Basics of workflow languages, writing CWL
What is CWL? First example
Running Tools Inside Docker
15:30 - 16:45 Combining tools in a workflow
Writing workflows
Scattering workflows
Part IV: Introduction to HYPATIA  
17:00 - 18:15 Using HYPATIA
18:15 - 18:45 Closing, discussion and Q&A


“ATHENA” Research Center (ATHENA RC)

Artemidos 6 & Epidavrou

15125, Marousi, GR

For more information, check the ATHENA RC contact page here.


License: CC BY 4.0

This material is made available under the Creative Commons Attribution 4.0 International license. Please see LICENSE for more details.


We acknowledge support of this work by the project “ELIXIR-GR: Managing and Analysing Life Sciences Data” (MIS: 5002780) which is implemented under the Action “Reinforcement of the Research and Innovation Infrastructure”, funded by the Operational Programme “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014-2020) and co-financed by Greece and the European Union (European Regional Development Fund).