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 nf-core and Nextflow	Understand core features of nf-core and Nextflow	20
	Running nf-core workflows	Learn how to pull Nextflow and nf-core pipelines from GitHub, how to run them, and how to inspect the Nextflow logs	50
	Break		10
	Configuring nf-core workflows	Understand how Nextflow is configured, how to write configuration files, and how to use parameters to modify the run	60
	Break		10
	Introduction to nf-core/rnaseq	Learn about nf-core/rnaseq and build a run command using required and optional parameters	60
2	Session 2 kick-off	Recap Session 1, discuss Session 2 learning outcomes and set up working space	10
	Customising with pipeline parameters	Use parameters to customise a run, track parameters with a run script and parameters file, and explore pipeline info files	70
	Break		10
	Question time		5
	Configuring resources for your environment	Configure compute resources for the workflow using custom configuration files	50
	Break		10
	Question time		5
	Customisation in action	Apply a number of customisation strategies to a theoretical real-world analysis scenario	70