Outgrown your laptop? Learn how to take your bioinformatics pipelines to the next level by scaling them on Australia’s national high performance computing (HPC) clusters.
In collaboration with the National Computational Infrastructure (NCI) and the Pawsey Supercomputing Research Centre, this hands-on workshop will equip you with the practical skills to run and optimise efficient Nextflow workflows on HPC systems.
Attendees will be guided through a series of hands-on exercises to configure nf-core workflows on NCI Gadi (PBS) and Pawsey Setonix (SLURM), and will iteratively develop a bioinformatics workflow to process larger files, and more samples.
Lead Trainers:
Dr Michael Geaghan, Senior Bioinformatician (Australian BioCommons), Sydney Informatics Hub (SIH), University of Sydney.
Fred Jaya, Senior Bioinformatician (Australian BioCommons), Sydney Informatics Hub (SIH), University of Sydney.
Date/Time: 18-19 November 2025, 1 - 4 pm AEDT /12:30 - 3:30 pm ACDT / 11 - 2 pm AWST
Format:
This online workshop will take place over two sessions of three hours each. You must attend both sessions in order to get the most out of the workshop. Expert trainers will introduce new topics and guide you through hands-on activities to help you put your new skills into action.
Learning outcomes:
By the end of the workshop you should be able to:
Identify the differences between traditional HPC job submission (e.g.sbatch, qsub) and workflow execution via Nextflow (e.g. how main jobs and child tasks map to HPC job schedulers)
Configure and execute scalable Nextflow workflows on HPC systems, selecting appropriate queues, nodes and job resources (CPU, memory, walltime) for large-scale parallel tasks
Manage software environments for reproducible workflows using tools like singularity, and adapt these to fit within different HPC ecosystem constraints
Monitor and troubleshoot Nextflow workflows on HPC systems, identifying and resolving errors related to configuration, resource allocation and environment setup
Who the workshop is for:
This workshop is for Australian researchers and technical users (bioinformaticians, life scientists, and data scientists) who:
Have access to HPC systems (e.g., institutional, national, or cloud-based clusters)
Have run simple Nextflow pipelines, typically in a one-sample-per-run or manual scripting context
Are now looking to scale up their workflows, optimise performance, and apply best practices for HPC environments
You must be associated with an Australian organisation for your application to be considered. Please note that participants will be supported with access to Gadi and Setonix computing resources for the duration of this workshop.
Prerequisites
Completed the “Hello Nextflow” workshop, or have equivalent experience (e.g. basic understanding of how to create and run a Nextflow pipeline)
Basic command line skills, such as manipulating files and running scripts and tools
Familiarity with concepts like multi-sample processing and reproducible analysis (e.g. containers)
Familiarity with how HPC clusters work (e.g., job submission, compute nodes)
Requirement for scalable analysis, running Nextflow on HPCs and schedulers
How to apply:
This workshop is free but participation is subject to application with selection.
Applications close at 11:59 pm AEDT, Monday 3 November 2025.
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.
This workshop is presented by Australian BioCommons with the assistance of a network of facilitators from the National Bioinformatics Training Cooperative. It is underpinned by computational resources provided by NCI and Pawsey Supercomputing Research Centre.
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