Fred Jaya
Ziad Al Bkhetan
Georgina Samaha

WORKSHOP: Hello Nextflow!

presented by Australian BioCommons and the Sydney Informatics Hub

The rise of big data has made it essential to be able to analyse and perform experiments on large datasets in a portable and reproducible manner. Nextflow is a popular bioinformatics workflow orchestrator that makes it easy to run data-intensive computational pipelines. It enables scalable and reproducible scientific workflows using software containers on any infrastructure. It allows the adaptation of workflows written in most languages and provides the ability to customise and optimise workflows for different computational environments, types and sizes of data.

This workshop will put you on the path to writing your own reproducible and scalable scientific workflows using Nextflow. You will learn how to use core Nextflow components to build, run and troubleshoot a simple multi-step workflow. There will be an opportunity to hear about the Australian Nextflow Seqera Service.

This workshop is not suitable for Linux/CLI beginners. If you are comfortable navigating the command-line, writing and modifying scripts, and familiar with basic workflow concepts, this workshop will help you take the next step in developing reproducible and automated workflows.

Learning outcomes: By the end of the workshop you should be able to:

• Describe and utlise core Nextflow components sufficient to build a simple multi-step workflow
• Describe next-step concepts such as operations and channels
• Launch a Nextflow workflow locally
• Find and interpret outputs and log files generated by Nextflow
• Troubleshoot basic issues

Prerequisites

This is an intermediate level workshop for people developing reproducible bioinformatics workflows. 

• Command line / linux skills are essential. The workshop will be conducted in a Unix environment.
• (Strongly recommended) Experience developing reproducible workflows (e.g. bash, CWL, WDL, or Snakemake)

Technical requirements

• Personal laptop with VS code installed (instructions will be provided closer to the date)
• Internet connection