workflow-clinic 0.9.0

AI-Powered Cloudification of Bioinformatics Workflows

Workflow Clinic

Workflow Clinic is a GSoC 2026 project focused on improving the portability, reproducibility, and cloud-readiness of scientific workflows.

The project aims to analyze workflow languages such as Nextflow and Snakemake, convert them into a common intermediate representation called WorkflowBundle, and identify workflow portability issues through automated validation and analysis.

By using a common workflow model inspired by the DAW (Data Analysis Workflow) metamodel, Workflow Clinic can reason about workflows independently of their original language and provide consistent diagnostics, recommendations, and future repair capabilities.

Why Workflow Clinic?

Scientific workflows are often tightly coupled to specific execution environments, storage systems, schedulers, or local infrastructure.

This can make workflows difficult to:

• Share
• Reproduce
• Port across platforms
• Execute in cloud environments
• Integrate with GA4GH-compliant services

Workflow Clinic aims to help workflow authors identify and resolve these issues before deployment.

Planned Features

Workflow Parsing

• Nextflow support
• Snakemake support
• Common WorkflowBundle representation

Workflow Analysis

• Portability diagnostics
• Storage validation
• Resource validation
• Metadata validation
• Workflow structure validation

AI-Assisted Review

• Rule-based workflow checks
• AI-assisted diagnostics
• Confidence-based recommendations

Workflow Repair

• Suggested fixes
• Automated transformations
• Validation of generated fixes

Installation

Clone the Repository

git clone https://github.com/revaarathore11/ga4gh_workflow_clinic_gsoc_2026-.git
cd ga4gh_workflow_clinic_gsoc_2026-

Create a Virtual Environment

python -m venv .venv
source .venv/bin/activate

Install Dependencies

pip install -e ".[dev]"

Development

Run Tests

pytest

Run Linting

ruff check .

Run Formatting

ruff format .

Supported Workflow Languages

Current target languages:

• Nextflow
• Snakemake

Potential future support:

• CWL
• WDL

Architecture Overview

Workflow Files
    ↓
  Parser
    ↓
WorkflowBundle
    ↓
Rule Engine
    ↓
 AI Critic
    ↓
  Doctor

Standards Alignment

Workflow Clinic is being designed with future compatibility in mind for:

• GA4GH TES
• GA4GH WES
• GA4GH TRS
• Workflow Run RO-Crate

License

This project is licensed under the Apache License 2.0.