aws-healthomics

name	aws-healthomics
description	Create, migrate, run, debug and optimize genomics workflows in AWS HealthOmics. Use when mentioning HealthOmics, WDL, CWL, Nextflow, genomics, or bioinformatics pipelines.

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"
      }
    }
  }
}