Janis – our portable pipelines project – end 2020 update

The Portable Pipelines Project started the development of Janis in late 2018 with the goal of delivering bioinformatics workflows that are portable and reproducible across many compute environments. Janis is a Python framework that provides a simple Application Programming Interface to build and run workflows that adhere to current standards of workflow specifications.

Over 2020, the team focused on expanding Janis’ community by running workshops, developing new pipelines and introducing more features to ease new users’ onboarding into the ecosystem.

2020 developments

  • The team developed workshop materials delivered at the Peter Mac workshops and the Bioinformatics Community Conference (BCC) 2020. In total, more than 50 participants have joined Janis workshops across these two events.
  • Janis has been integrated into Peter Mac automated bioinformatics analysis system, responsible for analysing hundreds of cancer sequencing samples every week across research and molecular pathology.
  • The number of tools and examples available in janis-bioinformatics has grown to more than 100 modules, with contributions from various institutes in Australia and overseas.
  • Introduced a new Janis development toolkit that enables importing of existing CWL pipelines into Janis, automated reference genome downloads, input validation and continuous integration tests of bioinformatics tools.

Community uptake

The project has continued its contribution to open source repositories including CWL, OpenWDL and Cromwell. In addition, Janis has now been included in the list of converters and code generators for CWL .

The project has also seen an increased uptake in cancer bioinformatics applications. A project involving multiple tumours from the same individual (CASCADE project) was recently analysed with workflows written in Janis (and this work has been submitted for publication). Melbourne Bioinformatics senior bioinformatician Assoc Prof Bernard Pope reports using Janis in his own work on Prostate Cancer through the PRECEPT project and a project investigating brain cancer with collaborators from Royal Melbourne Hospital, the Peter Doherty Institute and WEHI.

In 2020, Janis also welcomed a new collaboration with the Australian BioCommons, with a commitment to extend Janis’ use across the Australian research community.

Presentations

  • Bioinformatics Community Conference (BCC) 2020
  • WEHI seminar series
  • Monash Bioinformatics Platform Seminar
  • Somatic variant calling in whole genome sequencing, opportunities, challenges and solutions, Monash Partners Comprehensive Cancer Consortium, Tech Talks series, 20 November 2020
  • The Australian BioCommons Webinar series

Upcoming events

In 2021, more workshops on Janis will be scheduled to be run as part of the Parkville Bioinformatics Training Group’s activities led out of Melbourne Bioinformatics. This work will also extend beyond through the Australian BioCommons training program.

What’s next for Janis?

In 2021, the team looks to support more researchers to use Janis to analyse their data and build new workflows. The team aims to add new support for other workflow specifications, such as Nextflow, and continue to build more exemplar pipelines targeting other domains beyond cancer bioinformatics.