Best Practices for Building Nextflow Pipelines
Join International Nextflow expert Chris Hakkaart from Seqera for an in-person, interactive workshop on building Nextflow pipelines.
Chris will share best practices he and Seqera have gleaned over years of working with users across domains. Chris will be joined by local Seqera engineer, Marco De La Pierre.
This workshop is in-person only at the Pawsey Centre and is free for participants.
There is limited seating, so please register ONLY if you plan to attend for the entire day. Please arrive at 8:30am AWST to sign onto the system. Training starts promptly at 9:00am (AWST).
Who is this training for?
- Researchers, scientists, and developers who use Nextflow to build their computational pipelines
- ALL domains of research, including but not limited to life sciences, health sciences, genomics, radio astronomy, physics, chemistry, and CFD.
Pre-Requisites:
- Familiarity with the command line
- Such as understanding of file paths and basic command line functions (See this 30 min refresher from Pawsey)
- Familiarity with developing Nextflow pipelines
- Such as understanding the structure of a Nextflow workflow and process block. Familiarity with Session 1 of this training track is sufficient.
- Have a Github account
Agenda (Approximate):
Session 1: Brief Nextflow Refresher (3 hours; 9am-12noon AWST)
- An introduction to nextflow and nf-core (30 min)
- Introduction to channels, processes, and operators (1 hour)
- Break (15 min)
- Modularising pipelines (15 min)
- A crash course in Groovy (15 min)
- Introduction to nf-core tooling for pipeline development (30 min)
- Q&A (15 min)
Session 2: Building Pipelines (3 hours; 1pm-4pm AWST)
- Anatomy of an nf-core pipeline (15 min)
- nf-core tooling for developers (15 min)
- Adding modules and subworkflows (60 min)
- Break (15 min)
- nf-core schema and linting (30 min)
- Patched modules (30min)
- Q&A (15 min)
Meet Your Trainer:
Originally from New Zealand, Chris completed his undergraduate studies and PhD at the University of Otago. After working as a postdoc in New Zealand for a further 2 years he moved to Tübingen, Germany, and worked as a bioinformatician at the Institute for Medical Genetics and Applied Genomics. Chris joined Seqera in 2022 as a developer advocate and now works on a variety of projects that aim to strengthen the Nextflow and nf-core communities.