Hybrid workshop on CWL and Docker



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


  • Understand what containerisation is, and why you might use it in bioinformatics.
  • Be familiar with Docker; basic concepts and structure.
  • Find and run containers built by other people.
  • Build your own application into a container (containerisation).
  • Distribute your container online.


  • Understand syntax and structure for CWL.
  • Understand how to write CWL tool definitions for command line tools.
  • Read and write CWL files written in YAML.
  • How to run CWL workflows locally and on HYPATIA (formerly EG-CI).
  • Join CWL tools into a workflow.
  • Use Docker with CWL to provide software dependencies and ensure reproducibility.

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).


  • Experience in Shell; this includes basic commands (such as ls, cp, mv, nano/vim) and operations such as (apt, installing tools etc).

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