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PROOF (PRoduction On-ramp for Optimization and Feasibility) is a user-friendly tool designed for managing and executing WDL (Workflow Description Language) workflows using the Cromwell workflow manager, configured to run on the Fred Hutch cluster. PROOF allows users to:

  • Automate all the backend configurations necessary to run your workflows instantly.

  • Validate, troubleshoot, assess performance, and run their workflows all under one roof.

  • Refine their workflows before potential transitions to cloud-based infrastructures, providing a ‘proofing’ resource of sorts.

Getting Started

Training and Courses

Technical Documentation and Repositories

Release Notes

See our release notes in the PROOF repo for more details:

June 2024 - PROOF v1.0

What’s New

  • Users can now interact with data stored in S3 buckets within WDL workflows executed in PROOF! Just make sure to have your AWS CLI credentials established in Rhino and you can use the S3 path just like any other input.
  • GPU analysis is now possible via the gpu argument in your WDL task’s runtime section! For an example, try running this example script in the ww-test-workflows repo of the DaSL WILDS.
  • Additional features have been introduced to increase transparency in terms of the functionality of PROOF:
    • New /info API endpoint provides details on which code base is being used.
    • Server start date and time is now available on the “PROOF Server” tab.
    • Documentation links have been added to the “Welcome” tab and automated server creation email for increased visibility.


  • The default location of the Apptainer cache directory has been moved from scratch to /hpc/temp to avoid previously reported linkage issues associated with scratch.
    • If a user’s lab/group has not yet been onboarded to /hpc/temp, the cache location will default to the user’s home directory instead.
  • PROOF’s underlying WSGI server has been switched from Waitress to Gunicorn for better scalability and efficiency.
  • Session persistence or “stickiness” has been added to the Shiny app to ensure users only speak to one instance at a time.
  • Table entries that are longer than usual will now be abbreviated to 150 characters or less to ensure a consistent display.
  • A linting GitHub action has been added to the GitHub repository for improved CI/CD. All issues identified by this linting action have also been resolved.

February 2024 - PROOF v0.1

What’s New!

  • PROOF has now grouped together all the components for setting up and configuring your database and Cromwell server so you don’t have to manually configure each part!
  • You can interact with PROOF in two improved ways when running your workflows:
    • PROOF Shiny App - an easy to use interface for accessing and configuring workflows to run on our cluster
    • Through the R clients proofr and rcromwell - combined these allow you to run WDL workflows on PROOF from your R console
  • We’ve made some enhancements to the way you use PROOF including:
    • Each user must login with your Fred Hutch credentials so that no one else can access or use your Cromwell server session
    • Each user can only run one Cromwell server at a time so that you don’t lose track of your workflow sessions


  • No fixes just yet, we’re launching our product
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