Enabling reproducible and portable workflows: Janis
Being able to repeat analytical workflows consistently and accurately is critical in transferring and scaling methodologies, whether between research groups or for large-scale clinical use.
As part of the Australian BioCommons ‘Bring Your Own Data’ Expansion Project, a specialised framework is under development that creates simple workflow definitions that enable researchers and clinicians to work with different workflow languages.
‘Janis’ provides both a consistent language for describing workflows and a framework that can translate workflows between existing languages such as CWL and WDL. Originating from the Portable Pipelines Project between Melbourne Bioinformatics, the Peter MacCallum Cancer Centre, and the Walter and Eliza Hall Institute of Medical Research, BioCommons quickly saw the potential of supporting such a useful tool.
Janis will help make the work that biomedical researchers do more portable and less dependent on any particular technology.
A/Prof Bernie Pope
Australian BioCommons A/Director: Human Genome Informatics
Melbourne Bioinformatics Human Genomics Lead
Victorian Health and Medical Research Fellow
Janis is already being used by a number of groups, such as the Molecular Pathology Laboratory at the Peter MacCallum Cancer Centre where it helps manage workflows for the analysis of clinical cancer data on a significant scale. Melbourne Bioinformatics software engineer, Grace Hall, is currently working to extend Janis's ability to convert workflows from the popular Galaxy platform. Grace points out that research groups currently invest a lot of time and effort in creating workflows; translating them with Janis will make them easier to share, and maintain with minimal effort into the future. Richard Lupat, a bioinformatics software engineer from the Peter MacCallum Cancer Centre and one of the original Janis developers, says that translating to and from Nextflow, another widely used workflow language, will be the next goal.
More information about Janis can be found here.
This story was based on a news item first published in the Melbourne Bioinformatics newsletter.
The Australian BioCommons BYOD Expansion Project project is funded through NCRIS investments from Bioplatforms Australia and the Australian Research Data Commons (http://doi.org/10.47486/PL105) that are matched with co-investments from AARNet, Melbourne Bioinformatics, NCI, Pawsey, QCIF via the Queensland Government RICF fund, The University of Sydney, AGRF, Griffith University and Monash University.