Welcome to the AGM training day 2023

Reproducibility with Nextflow and nf-core

During this workshop we will establish the fundamental ideas and skills that are required for using Nextflow as a workflow manager. We will access an existing pipeline from the free repository nf-core and run this pipeline on a test dataset as an example.

The workshop is organised into three sections:

In session one we will provide an overview of Nextflow, introducing terminology, the format, and commands for working in the Nextflow environment.

In session two we will introduce nf-core - a repository of existing pipelines that can be easily accessed to quick-start an analysis. We will cover the general structure of a pipeline, and then use an example pipeline to familiarise you with running and customizing a workflow.

In the third and final session we will focus on that idea of customizing and configuring pipelines, as well as the metrics and shareable reports that you might generate during a workflow.

Generally speaking, this workshop is designed only as an introduction to Nextflow and aims to provide a persuasive argument for the use of a workflow manager. This workshop cannot be exhaustive, so at the end of the workshop I propose the creation of Nextflow group either on slack or github.

Finally, we will end the workshop with a short, standalone session on github use.