Creating private workflows in HealthOmics - AWS HealthOmics

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.

  • Parameter template file (optional): 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 container images for the workflow and store them in a private Amazon ECR repository.

  • Sentieon licenses (optional): 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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