Welcome to the mhubai-unleashed repository! This repository hosts WDL (Workflow Description Language) workflows for MHUBAI (Medical Hub AI), providing a structured and scalable way to run complex pipelines.

Please cite MHUBAI as this repo is based on their work: https://github.com/MHubAI

The workflows in this repository are designed to facilitate the execution of MHUBAI tasks, ensuring reproducibility and ease of use.

To get started with these workflows, follow these steps:

1. Visit our Dockstore page: MHUBAI Unleashed on Dockstore

2. Import the workflow to a platform of your choice:

   • DNANexus
   • Terra
   • elwazi
   • ANVIL
   • NHLBI BioData Catalyst

3. Provide the following inputs:

   • MHUBAI model name
   • aws or gcs urls in a txt or csv file, each line containing a single URL (choose one provider but not mix aws and gcp)
     • TIP: If files are downloaded from ImagingDataCommons, all SOPInstances in a series can be referenced by wildcard such as s3://idc-open-data/d0686cc8-0f8b-4e77-8707-605d1d8f7a08/*
   • If you want to override mhubai's default config, provide your custom config in yaml format while submitting the workflow

4. A sample data table manifest you can import can be found in the repo

   • Sample data table manifest