Healthomics

AWS HealthOmics

You have access to the AWS HealthOmics MCP server for creating, migrating, running, debugging, and optimizing genomics workflows.

When to Load Steering Files

When performing tasks related to the following scenarios, read the appropriate steering file from this skill's steering/ directory before proceeding:

• Creating a workflow from a Git repository URL (GitHub, GitLab, Bitbucket) → read steering/git-integration.md (takes precedence over workflow-development.md)
• Creating a new WDL, Nextflow, or CWL workflow from local files → read steering/workflow-development.md
• Running a deployed HealthOmics workflow → read steering/running-a-workflow.md
• Submitting, monitoring, or managing batch runs (multiple samples/runs at once) → read steering/batch-runs.md
• Onboarding an existing WDL workflow for HealthOmics compatibility → read steering/migration-guide-for-wdl.md
• Onboarding an existing Nextflow workflow for HealthOmics compatibility → read steering/migration-guide-for-nextflow.md
• Modifying, updating, or fixing an existing HealthOmics workflow → read steering/workflow-versioning.md
• Diagnosing workflow creation issues or run failures → read steering/troubleshooting.md
• Using public containers with HealthOmics via ECR Pull-Through Caches → read steering/ecr-pull-through-cache.md
• Using containers from registries not supported by ECR Pull-Through Cache (Seqera Wave, NVIDIA NGC, Google Artifact Registry) via image staging → read steering/image-staging.md
• Setting up VPC infrastructure for HealthOmics workflows → read steering/vpc-setup.md
• Managing HealthOmics VPC configurations (creating, listing, getting, or deleting) → read steering/healthomics-configuration.md
• Running workflows with VPC connectivity, public internet access, or cross-region access → read steering/vpc-connected-workflow-runs.md
• Understanding regional feature availability, GPU instance limitations, or troubleshooting region-specific errors → read steering/regional-capabilities.md

Onboarding

1. Ensure valid AWS credentials — The MCP server uses these to interact with AWS services.
2. Get the current account — Run aws sts get-caller-identity.
3. Create .healthomics/config.toml with run parameters:

omics_iam_role = "arn:aws:iam::<ACCOUNT_ID>:role/<HEALTHOMICS_ROLE_NAME>"
run_output_uri = "s3://<YOUR_BUCKET>/healthomics-outputs/"
run_storage_type = "DYNAMIC"

Ask the user for omics_iam_role and run_output_uri values, or offer to create them.

Dependencies

This configuration requires uvx (part of the uv Python package manager).