https://github.com/imagingdatacommons/mhubai-idc
https://github.com/imagingdatacommons/mhubai-idc
Last synced: 10 months ago
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- Host: GitHub
- URL: https://github.com/imagingdatacommons/mhubai-idc
- Owner: ImagingDataCommons
- License: mit
- Created: 2024-07-18T19:33:58.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2024-08-15T18:18:38.000Z (almost 2 years ago)
- Last Synced: 2025-03-12T15:51:12.769Z (about 1 year ago)
- Language: Jupyter Notebook
- Size: 8.32 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# MHUBAI Unleashed
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
## Overview
The workflows in this repository are designed to facilitate the execution of MHUBAI tasks, ensuring reproducibility and ease of use.
## Getting Started
To get started with these workflows, follow these steps:
1. Visit our Dockstore page: [MHUBAI Unleashed on Dockstore](https://dockstore.org/workflows/github.com/vkt1414/mhubai-unleashed/mhubaiDockerfileWorkflow:main?tab=info)
2. Import the workflow to a platform of your choice:
- [DNANexus](https://www.dnanexus.com/)
- [Terra](https://app.terra.bio/)
- [elwazi](https://elwazi.org/)
- [ANVIL](https://anvilproject.org/)
- [NHLBI BioData Catalyst](https://biocatalyst.nhlbi.nih.gov/)
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
5. A sample data table manifest you can import can be found in the repo
- [Sample data table manifest](https://github.com/vkt1414/mhubai-unleashed/blob/main/examples/mhubai_workflow.tsv)