INTRODUCTION TO NEXTFLOW

Online, 7-9 October 2024

Course website: https://www.physalia-courses.org/courses-workshops/course60/

Overview

Nextflow is a widely adopted workflow system for running high-throughput, data-intensive applications across cloud and on-premise infrastructure. It has fast become one of the primary technology platforms for computational workloads in life sciences.

The framework allows scientists to write code in any scripting language, define software dependencies with containers, connect tasks with the event-driven dataflow programming DSL and then deploy anywhere: local machines, grid computing systems or public cloud infrastructure.

Target audience and assumed background

The workshop is intended for users to become quickly proficient in Nextflow technology, starting from basic through to advanced concepts. The majority of the practicals will make use of command-line tools. Therefore familiarity with a *nix environment (e.g. Linux or MacOS) and the shell (e.g. Bash) are highly desirable.

PROGRAM

Monday- Classes from 2-8 pm CET

• Introduction to Nextflow
• Basic Scripting in Nextflow
• Channels
• Processes

Tuesday- Classes from 2-8 pm CET

• Operators
• Executors
• RNA-Seq pipeline
• Configuration
• Pipeline Parameter

Wednesday - Classes from 2-8 pm CET

• Workflows
• Modules
• Sharing Pipelines
• RNA-Seq pipeline 2

A repository will be provided with all the necessary material and software as well as an AWS cloud environment to carry out the activities in the relevant practical sessions.