‘Janis’ is now being used to analyse a mixture of whole genome and exome sequencing data at Peter Mac, WEHI & Melbourne Bioinformatics

Researchers across the Parkville Precinct and beyond now have a simpler way to run their data analysis pipelines on multiple computing platforms thanks to recent developments in the Portable Pipelines Project.

Over 2019, our team of experts across WEHI, PeterMac and Melbourne Bioinformatics built Janis, a new Python framework for building and running workflows. Janis provides a simple Application Programming Interface to build workflows that are portable and reproducible across many compute environments and it provides workflow specifications (Common Workflow Language [CWL] and Workflow Description Language [WDL]) as publishable artifacts.

2019 developments

  • Janis’ portability has been validated on systems at Peter Mac, WEHI, University of Melbourne, Pawsey Supercomputing Centre in WA and the Google Cloud Platform.
  • The project has generated considerable community awareness and support on GitHub and other online platforms.
  • Janis is in alpha testing now and is openly available for researchers to download and use through GitHub (support is available through GitHub and Gitter).
  • It is being successfully used by researchers at Peter Mac, WEHI and Melbourne Bioinformatics to analyse a mixture of whole genome and exome sequencing data.
  • Documentation now available here.

Community uptake

Uptake across the life science community has further validated Janis’ usefulness, with Kersten Breuer from the German Cancer Research Center adding support for Janis workflows to CWLab. And at a combined Broad Institute and AWS hackathon Janis was adopted to improve cloud support for Cromwell.

The project has now contributed to open source repositories including the CWL, WDL, Cromwell and more, and in particular the team has worked to document Singularity support for Cromwell.


  • Bioinformatics Open Source Conference (BOSC) 2019 – Basel
  • Victorian Bioinformatics Seminar (VCBS) 2019 – Melbourne
  • Australian Bioinformatics and Computational Biology Society (ABACBS) 2019 – Sydney
  • WEHI seminar series – Melbourne
  • Australian BioCommons briefing online across Australia

Upcoming events

In early 2020, workshops on Janis will run as part of the Parkville Bioinformatics Training Group’s activities led out of Melbourne Bioinformatics.

What’s next for Janis?

In 2020 the team is looking to support more researchers to use Janis to analyse their data and build new workflows. The team aims to build exemplar pipelines for analysing RNA seq data, run workshops, complete documentation and work closely with researchers to increase functionality.

This has been an exciting and productive collaboration to date. And given Janis is applicable for all research domains, it will also be interesting to see how it develops a life beyond its original intended use.