Description:

Nextflow is a workflow management tool designed to enable the creation of reproducible workflows that function across computational resources through the use of software containers. Many curated bioinformatics Nextflow pipelines can be found through the nf-core. In this workshop, we will explore their collection and work through running an nf-core pipeline on Quest. The biggest consideration for using Nextflow on Quest is setting the configuration to use Quest’s resources appropriately. We will cover how this is done through the nu-genomics profile for nf-core pipelines as well as writing a custom configuration file when necessary.

Prerequisite: This workshop requires a laptop with a terminal application installed and expects familiarity with working from the command line or attendance at the Command Line Introduction workshop.

About the series: This workshop series is designed to cover foundational topics in computational genomics for the research community that uses the Genomics Compute Cluster (GCC) at Northwestern. Most workshops can be attended ad hoc, but some of the content builds on itself from week to week, and most require attendance at the first workshop of the series, Command Line Introduction, so please read the description of each. These workshops will be held in person on the Chicago campus. To participate fully, you will need to bring a laptop with you to each workshop.