Bringing Seqera Platform to Australian researchers
Note: This activity completed in September 2024 with the launch of the Australian Nextflow Seqera Service.
Nextflow has emerged as a standard for defining bioinformatics workflows according to surveys undertaken by Australian BioCommons and collaborating partners. The importance of this bioinformatics workflow manager is also demonstrated with the increased use of Nextflow within ABLeS and Bioplatforms Australia framework communities, as well as the demand for Nextflow training.
Seqera Platform can support researchers wanting to use Nextflow bioinformatics workflows across a myriad of on-premise, supercomputing and commercial cloud platforms. Through a licence agreement with Seqera Labs, Australian BioCommons ran a pilot project for a national Nextflow Seqera Service that would enable a centralised command post for Nextflow pipelines to be offered as a fully subsidised service for Australian researchers.
The pilot program began in July 2022 as part of the Australian BioCommons Bring Your Own Data Expansion Project, with partners including Pawsey Supercomputing Research Centre (service hosts), NCI, SIH, QCIF and Melbourne Bioinformatics.
Aims of the pilot project
The pilot project had three key ambitions:
Establish a service where BioCommons early adopters, including both science and method communities, can easily run, manage and monitor the execution of Nextflow workflows on dedicated compute infrastructure.
Understand service demand and utilisation by working with BioCommons communities and assessing interest from other communities.
Develop service operational models; understand costs and benefits; develop a business case for continuing the service.
Pilot project outcomes
The Australian Nextflow Seqera Service was launched
Seqera Platform was deployed on Pawsey infrastructure
29 research groups were onboarded to the service (78 users from 16 different institutions).
The services were successfully integrated with our partner’s compute infrastructure such as NCI, Pawsey, on premises HPC, AWS and Azure
More than 334,000 jobs have been submitted to several compute infrastructures to perform 4,050 workflow executions.
Supported many groups with workflow development and deployment
Established a user guide
Promoted the service at conferences including Supercomputing Asia 2024 and the Nextflow Summit Barcelona 2023
Pilot project participants
Australian Genome Research Facility (AGRF) Bioinformatics team
Australian Amphibian and Reptile Genomics (AusARG) Phylogenomics Group
The Northcott Neuroscience Lab, ANZAC Research Institute
Bioinformatics Consulting Core Facility at the Peter MacCallum Cancer Centre
ZERO Childhood Cancer program at the Children's Cancer Institute
Garvan Institute of Medical Research’s Data Science Platform
P4 Respiratory Health for Kids Team at The Kids Research Institute
Queensland University of Technology’s eResearch Team
South Australian Genomics Centre at SAHMRI
Sydney Informatics Hub at the University of Sydney
Forrest Lab at the UWA Centre for Medical Research
Pilot project partners
