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.	40
	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.	15
	Break		10
	Configuring nf-core workflows	Understand how Nextflow is configured, how to write configuration files, and how to use Nextflow parameters to modify the run.	40
	Break		10
	Introduction to nf-core/rnaseq	Learn about nf-core/rnaseq and build a run command using required and optional parameters.	30
2	Session 2 kick-off	Discuss Session 2 learning outcomes and set up working space.	10
	Managing parameter reproducibility	Troubleshoot a pipeline warning message and apply a parameter file to track our parameters.	20
	Break		10
	Configuring a run for your environment	Configure compute resources for the workflow using a custom configuration file.	50
	Break		10
	Configurations to customise outputs	Apply multiple configuration files to customise various pipeline settings for the same run.	50