Nextflow for the Life Sciences
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 workshop schedule for the lesson plan.
Trainers
Facilitators
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.
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 | Arrival | |
| 13:15 | Welcome and housekeeping | |
| 13:25 | Introductions and icebreakers | |
| 13:40 | Workshop overview and setup | |
| 13:55 | Introduction to Nextflow (Part 1.0) | |
| 14:05 | Workshop: Part 1.1 - 1.4 | |
| 15:00 | BREAK | |
| 15:15 | Workshop: Part 1.5 - 1.8 | |
| 16:15 | Q&A and Day 1 recap |
Day 2
| Time (AEST) | Activity | Presenter(s) |
|---|---|---|
| 13:00 | Arrival | |
| 13:10 | Welcome and housekeeping | |
| 13:15 | Setup and introduction to Part 2 | |
| 13:25 | Workshop: Part 2.1 - 2.2 | |
| 14:15 | BREAK | |
| 14:30 | Workshop: Part 2.3 - 2.5 | |
| 15:50 | Day 2 summary | |
| 16:00 | Discussion and Q&A | |
| 16:15 | Wrap up and feedback 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. 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 Georgie Samaha, Giorgia Mori, Michael Geaghan, Fred Jaya, Mitchell O'Brien, Chris Hakkaart, Ziad Al-Bkhetan, Melissa Burke, Uwe Winter, Cali Willet, Matthew Downton, and Wenjing Xue.