Richard Lupat, Bioinformatician, PeterMac



Peter MacCallum Cancer CentreLEAD INSTITUTE
Australian BioCommonsCOLLABORATOR
Melbourne BioinformaticsCOLLABORATOR
Walter and Eliza Hall Institute of Medical ResearchCOLLABORATOR


PeterMac / WEHI / Melbourne Bioinformatics (University of Melbourne) / Australian BioCommons (via ARDC BYOD Expansion Project) co-funding

The Portable Pipelines Project (PPP) is a collaborative project between Peter MacCallum Cancer Centre, Melbourne Bioinformatics, WEHI and the Australian BioCommons that anticipates the complex needs of cancer (and other) researchers as whole genome sequencing (WGS) becomes routine in research and part of standard clinical evaluation of disease. It will do this by providing researchers with a modular, portable bioinformatics pipeline production and sharing system, capable of meeting current and future needs of WGS analysis.

Bench scientists working in cancer genomics are increasingly reliant upon data scientists. Data scientists in turn need to be able to choose the best practice analysis tools, problem-solve how to maximise access to scarce compute resources and bring their data management and curation discipline which is increasingly required for sharing data for publication, collaboration and reproducibility. This project aims to help with these problems through the development of Janis, a productivity framework implemented in Python with a simple API for the creation and translation of modular and robust portable pipelines using preeminent workflow descriptions that adhere to current standards, including Common Workflow Development language (CWL), Workflow Development Language (WDL), NextFlow and Galaxy. This allows workflows to be run on multiple computing platforms without the need to rewrite to accommodate multiple hardware systems from local HPC to cloud.

While motivated by WGS cancer research and pipelines, Janis can extend to other domains, making it an extremely useful tool which will be in demand by research teams worldwide.

For more information, see Janis.