Introduction to Nextflow and running nf-core workflows
This workshop is designed to provide participants with a foundational understanding of Nextflow and nf-core pipelines, with a focus on running existing pipelines efficiently. Participants are expected to have prior experience with the command-line interface and working with cluster systems like Slurm. The primary goal of the workshop is to equip researchers with the skills needed to use nf-core pipelines for their research data.
Course Presenters
- Song Li, Bioinformatics Core Facility, Peter Mac
- Richard Lupat, Bioinformatics Core Facility, Peter Mac
Course Helpers
- Emma Gail, Melbourne Bioinformatics
- Sanduni Rajapaksa, Research Computing Facility, Peter Mac
- Adam Taranto, WEHI
Prerequisites
- Experience with command line interface and cluster/slurm
- Familiarity with the basic concept of workflows
- Access to a slurm cluster
Learning Objectives:
By the end of this workshop, participants should be able to:
- Gain exposure to key concepts and terminology in Nextflow and nf-core pipelines.
- Understand the foundational knowledge required to navigate and customize the code base of nf-core pipelines.
- Develop basic troubleshooting and customization skills necessary for responsibly applying nf-core pipelines to your own research data
- Develop basic nextflow workflow
Set up requirements
Please complete the Setup Instructions before the course.
If you have any trouble, please get in contact with us ASAP.
Workshop schedule
| Lesson | Overview | Time |
|---|---|---|
| Setup | Follow these instructions to install VS Code and setup your workspace | Prior to workshop |
| Session kick off | Session kick off: Discuss learning outcomes and finalising workspace setup | 10:00 - 10.10 |
| Introduction to Nextflow | Introduction to Nextflow: Introduce nextflow’s core features and concepts; including CLI and how to run it on cluster | 10:10 - 10:25 |
| Introduction to nf-core | Key nf-core features and concepts, structures, tools, and example nf-core pipelines | 10:25 - 10:50 |
| Break | Break | 10:50 - 11:00 |
| Customising and running nf-core pipelines | Customising & running nf-core pipelines: Discuss pipelines’ required inputs, optional inputs, outputs, parameters file and configurations files | 11:00 - 11:30 |
| Troubleshooting a Nextflow run | Troubleshooting nextflow run: Discuss Nextflow logging, caching, task execution directory, dependencies, and manual troubleshooting | 11:30 - 12:00 |
| Lunch Break | Break | 12:00 - 12:45 |
| Introduction to processes and channels | Introduction to Nextflow channels types and process structure | 12:45 - 13:00 |
| Creating a basic Nextflow workflow | Introduction to nextflow channels, processes, data types and workflows | 13.00 - 13.45 |
| Best practise and Q&A | Best practise, tips & tricks for running nextflow pipelines | 13.45 - 14:00 |
Credits and acknowledgement
This workshop is adapted from various nextflow training materials, including: