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Hello Nextflow 2025

This workshop will provide you with the foundational knowledge required to build Nextflow workflows. The content is broken up into 2 parts. In the first part we will cover the basic principles for developing Nextflow pipelines. In the second part we will step through building our own Nextflow workflow. See the lesson plan for details.

Trainers

  • Fred Jaya, Sydney Informatics Hub, University of Sydney
  • Michael Geaghan, Sydney Informatics Hub, University of Sydney

Contributors

Prerequisites

This is an intermediate-advanced workshop for people developing reproducible bioinformatics workflows.

  • Experience working on the command line/Linux environment.
  • Experience developing reproducible workflows (e.g., bash, CWL, WDL, or Snakemake).

Set up requirements

Please complete the Setup instruction before the workshop. If you have any trouble, please get in contact with us ASAP via Slack.

Code of Conduct

In order to foster a positive and professional learning environment we encourage the following kinds of behaviours at all our events and on our platforms:

  • Use welcoming and inclusive language
  • Be respectful of different viewpoints and experiences
  • Gracefully accept constructive criticism
  • Focus on what is best for the community
  • Show courtesy and respect towards other community members
  • Our full code of conduct, with incident reporting guidelines, is available here.

Workshop schedule

Day 1

Time (AEST) Activity Presenter(s)
14:00 Welcome
14:10 Introduction to the workshop
14:15 Workspace set up 
14:20 Introduction to Nextflow and nf-core
14:30 Workshop: Part 1.0 - 1.4
15:30 BREAK
15:45 Workshop: Part 1.5 - 1.8
16:45 Q&A and Day 1 recap

Day 2

Time (AEST) Activity Presenter(s)
14:00 Day 2 Welcome
14:05 Setup and Introduction to Part 2
14:15 Workshop: Part 2.1 - 2.3
15:30 BREAK
15:45 Workshop: Part 2.4 - 2.5
16:40 Day 2 Summary
16:50 Wrap up and survey

Course survey

Please fill out our course survey at the end of the workshop. Help us help you! 😁

Credits and acknowledgements

This workshop event and accompanying materials were developed by the Sydney Informatics Hub, University of Sydney in partnership with Seqera. The workshop was enabled through the Australian BioCommons - BioCLI Platforms Project (NCRIS via Bioplatforms Australia).