Introduction to Workflow languages

20 October 2022 - 10am-3pm
21 Bedford St, North Melbourne, VIC 3051


Introduction to Workflow languages

This hands on workshop demonstrates how to write workflows using a workflow language.

Workshop Description:

This workshop demonstrates how to write workflows using a workflow language. An introduction to workflow theory, implementation using the CWL language, and execution on a compute environment will be demonstrated. By the end of the session, participants will be able to write and execute basic workflows in CWL. Participants will also gain experience migrating an existing workflow from one system (Galaxy) to another (CWL). Skills learned will be easily transferable to other workflow languages (eg Nextflow) participants may want to learn in the future. Workflow systems have become a core aspect of research over time. Most researchers will run a repeatable analysis requiring multiple software tools during their career. For this reason, skills involving developing, running and maintaining workflows are continuing to be valuable in our industry. A number of workflow systems are currently popular, including Galaxy, CWL, WDL and Nextflow. While Galaxy is the easiest system to get started with, it is not suitable for all workflows and all data. In these cases, researchers may need to use a dedicated workflow language, rather than a system like Galaxy. A few examples:
  • Galaxy server does not permit certain data being run (sensitive data)
  • Galaxy server does not have required software tool installed, and would be highly time consuming to develop a wrapper
  • Galaxy server may not offer the required amount compute resources
This workshop will train participants how to use the CWL workflow language as a solution to these cases.


Grace Hall (Melbourne Bioinformatics, The University of Melbourne)

Richard Lupat (Bioinformatics Core Facility, Peter MacCallum Cancer Centre )

Target audience:

This workshop is aimed at Bioinformaticians who wish to learn how to use a workflow language (CWL). Familiarity with command line and a programing language is required.


This free workshop is available to staff and students at The University of Melbourne and its affiliated institutes only (refer to ‘Members’ section).

When registering for this event you must provide an email address for an affiliated institutional, or your registration may be cancelled.


This is an in person hands-on workshop and attendees must bring their own computers (and charges) with access to WiFi.

This workshop will involve writing workflows using CWL and running command line tools. The following is highly recommended:

  • Basic familiarity with a programming language (ie Python, R, Javascript)
  • Command line familiarity (can move around folders, run bioinformatics tools)
  • Basic familiarity with docker / containers


If you require any further information, or have any access requirements in order to participate in this workshop, please contact the workshop organiser Melbourne Bioinformatics as soon as possible to discuss your requirements: