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.

It is not intended for those looking to develop new Nextflow workflows

Course Presenters

• Richard Lupat, Bioinformatics Core Facility
• Miriam Yeung, Cancer Genomics Translational Research Centre

Course Helpers

• Sanduni Rajapaksa, Research Computing Facility
• Song Li, Bioinformatics Core Facility
• Henrietta Holze, Dawson Lab

Prerequisites

• Experience with command line interface and cluster/slurm
• Familiarity with the basic concept of workflows
• Access to Peter Mac 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.

Set up requirements

Please complete the Setup Instructions before the course.

If you have any trouble, please get in contact with us ASAP via Slack/Teams.

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	09:30 - 09:40
Introduction to Nextflow	Introduction to Nextflow: Introduce nextflow’s core features and concepts; including CLI and how to run it on Peter Mac cluster	09:40 - 10:20
Introduction to nf-core	Introduction to nf-core: Introduce nf-core features and concepts, structures, tools, and example nf-core pipelines	10:20 - 11:00
Break	Break	11:00 - 11:15
Customising & running nf-core pipelines	Customising & running nf-core pipelines: Discuss pipelines’ required inputs, optional inputs, outputs, parameters file and configurations files	11:15 - 11:45
Troubleshooting nextflow run	Troubleshooting nextflow run: Discuss Nextflow logging, caching, task execution directory, dependencies, and manual troubleshooting	11:45 - 12:15
Best practise and Q&A	Best practise, tips & tricks for running nextflow pipelines at Peter Mac cluster	12:15 - 12:45

Credits and acknowledgement

^{This workshop is adapted from Customising Nf-Core Workshop materials from Sydney Informatics Hub}