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 scalable multi-step workflow.
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
Develop a scalable workflow that processes multiple samples and incorporates advanced features
Assess the effectiveness of a workflow in handling multiple samples in parallel execution.
Lead Trainers:
Dr Chris Hakkaart, Developer Advocate, Seqera Labs.
Fred Jaya, Senior Bioinformatician (Australian BioCommons), Sydney Informatics Hub, University of Sydney.
Dr Georgie Samaha - Product Owner of the Australian BioCommons BioCLI Project and Bioinformatics Group Lead at the Sydney Informatics Hub, The University of Sydney.
Date/Time: 24 - 25 September 2024, 2 - 5 pm AEST/ 1:30 - 4:30pm ACST / 12 - 3 pm AWST
Location: Online
Format:
This online workshop will take place over two 3 hour sessions. You must attend both sessions in order to get the most out of the workshop. Expert trainers will introduce new topics and guide you through hands-on activities to help you put your new skills into action.
Who the workshop is for:
This is an intermediate-advanced workshop for people developing reproducible bioinformatics workflows.
Prerequisites
You must be associated with an Australian organisation for your application to be considered
Command line / linux experience is essential. The workshop will be conducted in a Unix environment
Experience developing reproducible workflows (eg. bash, CWL, WDL, or Snakemake)
Experience with Github and a Github account
How to apply:
This workshop is free but participation is subject to application with selection.
Applications have closed
Applications are reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date. More information on the selection process is provided in our Advice on applying for Australian BioCommons workshops.
This workshop is presented by Australian BioCommons, the Sydney Informatics Hub and Seqera with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
This event is part of a series of bioinformatics training events. If you'd like to hear when registrations open for other events, please subscribe to the Australian BioCommons newsletter
Cover image: Nextflow logo