| name | aws-healthomics |
| description | 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 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"
