Translating workflows into Nextflow with Janis
Channel: Australian BioCommons
Date: 2023-06-23

This video includes presentations and demonstrations from the Australian BioCommons workshop 'Translating workflows into Nextflow with Janis' which took place on 19 June 2023.

The training materials from the workshop are available here:

https://www.melbournebioinformatics.org.au/tutorials/tutorials/janis_translate/janis_translate

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Workshop description

Bioinformatics workflows are critical for reproducibly transferring methodologies between research groups and for scaling between computational infrastructures. Research groups currently invest a lot of time and effort in creating and updating workflows; the ability to translate from one workflow language into another can make them easier to share, and maintain with minimal effort. For example, research groups that would like to run an existing Galaxy workflow on HPC, or extend it for their use, might find translating the workflow to Nextflow more suitable for their ongoing use-cases. 

Janis is a framework that provides an abstraction layer for describing workflows, and a tool that can translate workflows between existing languages such as CWL, WDL, Galaxy and Nextflow. Janis aims to translate as much as it can, leaving the user to validate the workflow and make small manual adjustments where direct translations are not possible. Originating from the Portable Pipelines Project between Melbourne Bioinformatics, the Peter MacCallum Cancer Centre, and the Walter and Eliza Hall Institute of Medical Research, this tool is now available for everyone to use.

This workshop provides an introduction to Janis and how it can be used to translate Galaxy and CWL based tools and workflows into Nextflow. Using hands-on examples we’ll step you through the process and demonstrate how to optimise, troubleshoot and test the translated workflows.
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Lead Trainers: 

Grace Hall, Software Engineer, Melbourne Bioinformatics

Richard Lupat, Senior Bioinformatics Software Engineer, Peter MacCallum Cancer Centre

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Who the workshop is for:

This workshop is for researchers and bioinformaticians who are using and/or customising workflows. It is conducted in a Unix environment. Command line experience is required. Prior experience with developing, running, and troubleshooting Nextflow workflows is strongly recommended.

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