The rise of big data has made it essential to be able to analyse and perform experiments on large datasets in a portable and reproducible manner. Nextflow is a popular bioinformatics workflow orchestrator that makes it easy to run data-intensive computational pipelines. It enables scalable and reproducible scientific workflows using software containers on any infrastructure. It allows the adaptation of workflows written in most languages and provides the ability to customise and optimise workflows for different computational environments, types and sizes of data.
Learn to build reproducible and scalable scientific workflows with Nextflow in this two-part workshop. Part one covers the fundamental principles of Nextflow pipeline development using the “Hello Nextflow” materials. Part two offers practical, hands-on experience creating a multi-sample Nextflow workflow for RNAseq data preparation.
Learning outcomes:
By the end of the workshop you should be able to:
Describe and use core Nextflow components sufficient to build a simple multi-step workflow
Describe next-step concepts such as operations and channels
Launch a Nextflow workflow locally
Find and interpret outputs and log files generated by Nextflow
Troubleshoot basic issues
Develop a scalable workflow that processes multiple samples and incorporates advanced features
Assess the effectiveness of a workflow in handling multiple samples in parallel execution
Lead Trainers:
Fred Jaya, Senior Bioinformatician (Australian BioCommons), Sydney Informatics Hub, University of Sydney.
Dr Michael Geaghan, Senior Bioinformatician (Australian BioCommons), Sydney Informatics Hub, University of Sydney.
Date/Time: 22 - 23 July 2025, 1-5pm AEST/ 12:30-4:30pm ACST / 11-3pm AWST
Format:
This workshop will take place over two sessions via a distributed training methodology.
Participants will join in person satellite sites at host universities and research institutes across Australia which will connect via Zoom with lead trainers Fred Jaya and Michael Geaghan. All sites will be supported by experienced local facilitators, who will guide you through hands-on activities and help you put your new skills into action
Satellite sites will be located in central locations in:
Brisbane
Sydney
Perth
Adelaide
Melbourne
Canberra
If travel is an impediment to participating, please get in touch (training@biocommons.org.au) to discuss alternative options.
Who the workshop is for:
This is a workshop for people developing reproducible bioinformatics workflows.
Prerequisites
You must be associated with an Australian organisation for your application to be considered
Command line / linux skills are essential. The workshop will be conducted in a Unix environment.
Experience developing reproducible workflows (e.g. bash, CWL, WDL, or Snakemake)
Experience with Github and a Github account
How to apply:
This workshop is free but participation is subject to application with selection. During the application process you must choose the satellite site you would like to join.
Applications close at 11:59pm AEST, Friday 27 June 2025.
Applications are reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). More information on the selection process is provided in our Advice on applying for Australian BioCommons workshops.
This workshop is presented by Australian BioCommons and the Sydney Informatics Hub 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 the Australian BioCommons newsletter.