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 (EG-CI).


Maximum participants: 25


Day 1

Time Details
10:00 - 10:30 Tutorial introduction.

- Get to know each other.
- Setup
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Part I: Containers Background  
10:30 - 11:30 Introduction to Containerization.

- Concepts and Theory
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11:45 - 13:00 Run a container.

- Examples of how to run an existing Docker container
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Part II: Building a Container  
14:00 - 15:30 Building a container image.

- How to build a container
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15:45 - 17:00 Distribute online

- What are the available options (DockerHub, GitHub)
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17:00 Closing, discussion and feedback

Day 2

Time Details
09:00 - 09:30 Welcome back and Q&A.

- Recap of Day 1
- Setting up for Day 2
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Part I: Basics of Workflow Languages  
09:30 - 10:45 Intro to workflows.

- Syntax and structure of CWL
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11:00 - 12:30 Writing a CWL in YAML.

- Examples of tool definitions in CWL
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Part II: Hands-on  
13:30 - 14:45 Combining tools in a workflow.

- Building a complete workflow in CWL
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15:00 - 16:30 Deploying a tool on EG-CI

- Using the ELIXIR-GR e-infrastructure?
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16:30 - 17:00 Closing, discussion and Q&A


Dates of the workshop: 30-31/03/2020 (Postponed due to COVID-19)

Please register to the workshop using this form.

Deadline: Mon 16/03/2020 (tba)

Notifications: Wed 18/03/2020 (tba)


National Infrastructures for Research and Technology (GRNET)

Kifisias Avenue 7

115 23, Athens, GR

30-31 March, 2020

For more information, check the GRNET contact page here

Other examples

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Sources / References

The material in the workshop has been based on the following resources:

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Relevant literature includes:

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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.


This work has been produced with the support of the RDA Europe Ambassador programme. It has received funding from the European Union’s Horizon 2020 (H2020) research and innovation programme via the RDA EU 4.0 project (ref. GA no. 777388).