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 - VPC setup →
references/vpc-setup.md - VPC configuration →
references/healthomics-configuration.md - VPC connected runs →
references/vpc-connected-workflow-runs.md
Onboarding
- Ensure valid AWS credentials are configured.
- Run
aws sts get-caller-identityto 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"