AWS HealthOmics variant stores and annotation stores will no longer be open to new customers starting November 7th, 2025. If you would like to use variant stores or annotation stores, sign up prior to that date. Existing customers can continue to use the service as normal. For more information, see AWS HealthOmics variant store and annotation store availability change.
Creating private workflows in HealthOmics
Private workflows depend on a variety of resources that you create and configure before creating the workflow:
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Workflow definition file: A workflow definition file written in WDL, Nextflow, or CWL. The workflow definition specifies the inputs and outputs for runs that use the workflow. It also includes specifications for the runs and run tasks for your workflow, including compute and memory requirements. The workflow definition file must be in
.zipformat. For more information, see Workflow definition files.-
You can use Amazon Q CLI to build and validate your workflow definition files in WDL, Nextflow, and CWL. For more information, see Example prompts for Amazon Q CLI and the HealthOmics Agentic generative AI tutorial
on GitHub.
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(Optional) Parameter template file: A parameter template file written in JSON. Create the file to define the run parameters, or HealthOmics generates the parameter template for you. For more information, see Parameter template files for HealthOmics workflows.
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Amazon ECR container images: Create a private Amazon ECR repository for the workflow. Create container images in the private repository, or synchronize the contents of a supported upstream registry with your Amazon ECR private repository.
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(Optional) Sentieon licenses: Request a Sentieon license to use the Sentieon software in private workflows.
Optionally, you can run a linter on the workflow definition before or after you create the workflow. The linter topic describes the linters available in HealthOmics.
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