Creating or updating a workflow - AWS HealthOmics

Creating or updating a workflow

To create a private workflow, you need:

  • 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.

For workflow definition files larger than 4 MiB (zipped), choose one of these options during workflow creation:

  • Upload to an Amazon Simple Storage Service folder and specify the location.

  • Upload to an external repository (max size 1 GiB) and specify the repository details.

After you create a workflow, you can update the following workflow information with the UpdateWorkflow operation:

  • Name

  • Description

  • Default storage type

  • Default storage capacity (with workflow ID)

  • README.md file

To change other information in the workflow, create a new workflow or workflow version.

Use workflow versioning to organize and structure you workflows. Versions also help you to manage the introduction of iterative workflow updates. For more information about versions, see Create a workflow version.

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