Creating private workflows in HealthOmics

Private workflows depend on a variety of resources that you create and configure before creating the workflow:

• 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 .zip format. For more information, see Workflow definition files in HealthOmics.

  • 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.

• (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.

• 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.

• (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.

Topics

• Workflow definition files in HealthOmics

• Parameter template files for HealthOmics workflows

• Container images for private workflows

• Requesting Sentieon licenses for private workflows

• Workflow linters in HealthOmics

• Creating or updating a workflow