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:
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Visit our Dockstore page: MHUBAI Unleashed on Dockstore
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Import the workflow to a platform of your choice:
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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
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A sample data table manifest you can import can be found in the repo