Welcome to the workshop!

In this workshop, we explore Nextflow and nf-core as powerful tools for bioinformatics data processing pipelines. Our goal for this workshop is to provide you with foundational knowledge required to understand the code base of any nf-core pipeline and responsibly apply and customise an nf-core pipelines to your own research.

These sessions will provide you with an opportunity to develop your skills and get exposure to key concepts in Nextflow and nf-core pipelines. Even if you are already familiar with Nextflow and have some experience with nf-core pipelines, it will take you time and practice beyond this workshop to fully understand the concepts and terminology laid out here.

Lesson plan

Session	Lesson	Outcomes	Time (min)
1	Session 1 kick-off	Discuss session 1 learning outcomes and set up working space.	10
	Introduction to Nextflow	Understand core features of Nextflow and learn fundamental Nextflow options and features.	40
	Introduction to nf-core	Understand core features of nf-core and learn how to use nf-core tools utility.	15
	Break	☕	15
	Configuring nf-core workflows	Understand the structure of an nf-core pipeline and the use of customisation options.	40
	Commands for users	Apply the nf-core tools utility’s list, download, and launch commands.	30
2	Session 2 kick-off	Discuss session 2 learning outcomes and set up working space.	10
	Design a run command	Build a run command for the nf-core/rnaseq pipeline using required and optional parameters.	30
	Reproducible parameters	Troubleshoot a pipeline warning message and apply a parameter file to track our parameters.	20
	Break	☕	15
	Configure compute resources	Configure compute resources for the workflow using a custom configuration file.	50
	Apply multiple configurations	Apply multiple configuration files to customise various pipeline settings for the same run.	50

All materials copyright Sydney Informatics Hub, University of Sydney