How do I install the AWS Healthomics skill?

Run npx skillmds@latest add aws-samples/aws-healthomics in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is AWS Healthomics safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with AWS Healthomics?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is AWS Healthomics free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published AWS Healthomics?

aws-samples (@aws-samples) published this skill. Their other Agent Skills are listed on their SkillMD profile.

AWS Healthomics by aws-samples — Agent Skill

Name: AWS Healthomics
Author: aws-samples

AWS Healthomics

Create, migrate, run, debug, and optimize genomics workflows in AWS HealthOmics. Use when the user asks about HealthOmics, WDL, Nextflow, CWL, genomics pipelines, or bioinformatics workflows on AWS.

aws-samples eb1b7b4 15 files · 137.9 KB Updated Sep 17, 2026

File contents

AWS HealthOmics Skill

This skill provides procedural knowledge for working with AWS HealthOmics workflows via the MCP server.

Available Workflows

Load the appropriate reference file based on the task:

Create from Git repo → references/git-integration.md
Create from local files → references/workflow-development.md
Run a workflow → references/running-a-workflow.md
Batch runs → references/batch-runs.md
Migrate WDL → references/migration-guide-for-wdl.md
Migrate Nextflow → references/migration-guide-for-nextflow.md
Version/update workflow → references/workflow-versioning.md
Troubleshoot failures → references/troubleshooting.md
ECR containers → references/ecr-pull-through-cache.md
Stage container images → references/image-staging.md
VPC setup → references/vpc-setup.md
VPC configuration → references/healthomics-configuration.md
VPC connected runs → references/vpc-connected-workflow-runs.md
Regional capabilities → references/regional-capabilities.md

Onboarding

Ensure valid AWS credentials are configured.
Run aws sts get-caller-identity to verify the account.
Check for or create .healthomics/config.toml:

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

Frequently asked questions