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Reproducibility with Nextflow and nf-core

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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 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 where you can discuss your projects.

Attribution notice

The workshop content was inspired by material written for Foundational Nextflow Training and the Reproducible workflows with nf-core run by Sydney Informatics Hub, University of Sydney.