whchoi98 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
- Ensure valid AWS credentials
- Get account number:
aws sts get-caller-identity - Create
.healthomics/config.tomlwith omics_iam_role and run_output_uri - Requires
uvxinstalled
MCP Server Config
{
"mcpServers": {
"healthomics": {
"command": "uvx",
"args": ["awslabs.aws-healthomics-mcp-server@latest"],
"env": {
"AWS_PROFILE": "default",
"AWS_REGION": "us-east-1"
}
}
}
}