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.

Learning outcomes:

By the end of the workshop you should be able to:

• Recognise the main aspects and benefits of workflow translation
• Use Janis to translated Galaxy / CWL tools & workflows to Nextflow
• Configure Nextflow to run translated tools & workflows
• Troubleshoot translated Nextflow tools & workflow
• Adjust the translated Nextflow tools / workflows & complete missing translations manually

Lead Trainers:

Grace Hall, Software Engineer, Melbourne Bioinformatics

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

Date/Time: 19 June 2023, 1 - 4:30pm AEST/12:30 - 4:00pm ACST /11am - 2:30pm AWST

Format:

This workshop will take place online. Expert trainers will introduce new topics and guide you through hands-on activities in breakout rooms to help you put your new skills into action.

Who the workshop is for:

This workshop is for Australian researchers and bioinformaticians who are using and/or customising workflows. You must be associated with an Australian organisation for your application to be considered.

The workshop will be conducted in a Unix environment. Command line experience is required. Prior experience with developing, running, and troubleshooting Nextflow workflows is strongly recommended. You may wish to attend our workshop Unlocking nf-core - customising workflows for your research in advance.

If you’re looking for an introduction to the fundamentals of Nextflow and nf-core you can watch our webinar Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud or recordings of recent nf-core training.

How to apply:
This workshop is free but participation is subject to application with selection.

Applications close at 11:59pm AEST, 4 June 2023.

Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date. More information on the selection process is provided in our advice on applying for Australian BioCommons workshops.

Apply here

This workshop is presented by the Australian BioCommons with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.

This event is part of a series of bioinformatics training events. If you'd like to hear when registrations open for other events, please subscribe to Australian BioCommons