Dr Evan Floden

Building foundational infrastructure tooling for open science

Abstract will be published shortly

WORKSHOP: Introduction to writing reproducible workflows with Nextflow

Nextflow is an open-source workflow framework for writing and scaling data-intensive computational pipelines. It is designed around the Linux philosophy of simple yet powerful command-line and scripting tools that, when chained together, facilitate complex data manipulations. Combined with support for containerization and both on-premise architectures and major cloud providers, Nextflow simplifies the writing and deployment of complex data pipelines on any infrastructure.

This hands-on workshop will give participants an overview of the motivations for using a workflow manager and outlines the key features of Nextflow. Participants will become familiar with basic Nextflow concepts of Channels, Processes and Operators and be guided through implementing a proof-of-concept RNA-seq pipeline.

Keywords: Workflow manager, pipelines, Nextflow

Requirements: Participants can install requirements locally or use our preconfigured Gitpod environment. The requirements for each environment are outlined below.

Local installation (best if you are already familiar with Git and Docker):

• Bash
• Java 11 (or later, up to 18)
• Git
• Docker
• Internet connection

Gitpod (best for first-timers and free for up to 50 hours per month):

• A GitHub account
• Web browser (e.g., Google Chrome or Firefox)
• Internet connection

Assumed knowledge: Familiarity with the command line and a basic understanding of scripting language concepts is assumed. Prior experience with Nextflow is not required.

Relevance: This workshop is intended for anyone interested in writing reproducible workflows with Nextflow.