Processing and analysing ‘omics datasets poses many challenges to life scientists, particularly when we need to share our methods with collaborators and scale up our research. Public and reproducible bioinformatics workflows, like those developed by nf-core, are therefore invaluable resources for the life science community.
nf-core is a community-driven effort to provide high-quality bioinformatics workflows for common analyses including, RNAseq, mapping, variant calling, and single cell transcriptomics. A big advantage of using nf-core workflows is the ability to customise and optimise them for different computational environments, types and sizes of data, and research goals.
This workshop will set you up with the foundational knowledge required to run and customise nf-core workflows in a reproducible manner. Over two days you will learn about the nf-core tools utility, step through the code structure of nf-core workflows, and explore the various ways to adjust workflow parameters, customise processes, and configure workflows for your computational environment, using the nf-core/rnaseq workflow as a hands-on example.
Lead Trainers:
Dr Cali Willet, Senior Bioinformatician, Sydney Informatics Hub, University of Sydney
Dr Michael Geaghan, Senior Bioinformatician, Sydney Informatics Hub, University of Sydney
Date/Time: 27-28 May 2026, 12 - 4 pm AEST /11:30 - 3:30 pm ACST / 10 - 2 pm AWST (Check in your timezone)
Location: Online
Learning outcomes:
By the end of the workshop you should be able to:
Explain the roles of Nextflow and nf-core in enabling reproducible and portable bioinformatics
Navigate thee nf-core directory structure to identify key configuration files
Write and run a basic nf-core run command
Modify command-line arguments to customise the workflow
Describe Nextflow configuration hierarchy
Create and use a params file to customise workflow parameters
Create and use a custom config file to adjust resource usage
Apply external arguments not available as a workflow parameter to a process
Who the workshop is for:
This workshop is for life science researchers and bioinformaticians who are already (or soon will) be using and customising nf-core workflows. You must be associated with an Australian organisation for your application to be considered.
Prerequisites
Recommended: New to Nextflow and containers? We highly recommend reviewing the resources below to help you get the most out of the workshop.
For a general overview on containers, you can view the Pawsey Supercomputing Centre training courses:
For an introduction to the fundamentals of Nextflow syntax and optimisation, you can view our Nextflow workshop materials:
Additionally, Seqera has developed a comprehensive suite of Nextflow training resources.
Required: Experience working in a Linux-based command-line environment and basic command line skills, including writing scripts and running tools.
How to apply:
This workshop is free but participation is subject to application with selection.
Applications close at 11:59 pm AEST, 13 May 2026.
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.