Workshops and courses

WORKSHOP: Nextflow for the life sciences

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Date: 22 - 23 July 2025

Timezone: Melbourne

Duration: 3 hours

Language of instruction: English

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.

Format

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

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

Who the workshop is for:

This is a workshop for people developing reproducible bioinformatics workflows.

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.

Apply here.

Contact: training@biocommons.org.au

Keywords: Bioinformatics, Nextflow

City: - Brisbane - Sydney - Perth - Adelaide - Melbourne - Canberra

Country: Australia

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

Learning objectives:

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

Organizer: Australian BioCommons

Host institutions: Australian BioCommons

Eligibility:

  • Registration of interest

Event types:

  • Workshops and courses

Cost basis: Free to all

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