Nextflow for the Life Sciences 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 event description and workshop schedule for learning outcomes and lesson plan, respectively.
Trainers
- Fred Jaya, Sydney Informatics Hub, University of Sydney
- Michael Geaghan, Sydney Informatics Hub, University of Sydney
Facilitators
| Site | Facilitator(s) |
|---|---|
| Brisbane (QCIF/QUT) | Magdalena Antczak, Marie-Emilie Gauthier |
| Perth (Pawsey) | Sarah Beecroft, Pratihba Raghunandan |
| Canberra (NCI) | Kisaru Liyanage |
| Adelaide (SAGC) | John Salamon |
| Melbourne (Melbourne Bioinformatics) | Emma Gail, Grace Hall |
| Melbourne (Peter MacCallum Cancer Centre) | Richard Lupat |
| Sydney (Garvan Institute of Medical Research) | Thanh Nguyen, Eric Urng |
Prerequisites
This is an intermediate-advanced workshop for people developing reproducible bioinformatics workflows. It assumes some experience with the following:
- Experience working on the command line/Linux environment.
- Experience with basic scripting (e.g. Bash).
In addition, experience with other reproducible workflow tools (e.g. CWL, WDL, or Snakemake) will be very useful, although not at all required for this workshop.
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) |
|---|---|---|
| 13:00 | Welcome | Giorgia |
| 13:10 | Introduction to the workshop | Giorgia, Fred |
| 13:15 | Workspace set up | Fred |
| 13:20 | Introduction to Nextflow (Part 1.0) | Fred |
| 13:30 | Workshop: Part 1.1 - 1.4 | Fred |
| 14:30 | BREAK | Giorgia |
| 14:45 | Workshop: Part 1.5 - 1.8 | Fred |
| 15:45 | Q&A and Day 1 recap | Fred, Giorgia |
Day 2
| Time (AEST) | Activity | Presenter(s) |
|---|---|---|
| 13:00 | Day 2 Welcome | Giorgia |
| 13:05 | Setup and Introduction to Part 2 | Michael |
| 13:15 | Workshop: Part 2.1 - 2.3 | Michael |
| 14:30 | BREAK | Giorgia |
| 14:45 | Workshop: Part 2.4 - 2.5 | Michael |
| 15:40 | Day 2 Summary | Michael, Giorgia |
| 15:50 | Wrap up and survey | Giorgia |
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. The workshop was enabled by Australian BioCommons' BioCLI Platforms Project (NCRIS via Bioplatforms Australia). Compute resources were provided by the National Computational Infrastructure (NCI).
We gratefully acknowledge the contributions of Chris Hakkaart, Ziad Al-Bkhetan, Melissa Burke, Giorgia Mori, Uwe Winter, Georgie Samaha, Cali Willet, Mitchell O'Brien, Matthew Downton, and Wenjing Xue.
