aws-healthomics

AWS HealthOmics

Overview

Create, migrate, run, debug and identify optimization opportunities for genomics workflows (WDL, Nextflow, CWL) in AWS HealthOmics.

When to Use

• Creating workflows from Git repos or local files
• Running deployed HealthOmics workflows
• Batch runs (multiple samples)
• Migrating existing WDL/Nextflow workflows
• Diagnosing workflow creation issues or run failures
• Using public containers via ECR Pullthrough Caches

Setup

1. Ensure valid AWS credentials
2. Get account number: aws sts get-caller-identity
3. Create .healthomics/config.toml with omics_iam_role and run_output_uri
4. Requires uvx installed

MCP Server Config

{
  "mcpServers": {
    "healthomics": {
      "command": "uvx",
      "args": ["awslabs.aws-healthomics-mcp-server@latest"],
      "env": {
        "AWS_PROFILE": "default",
        "AWS_REGION": "us-east-1"
      }
    }
  }
}