Private workflows - AWS HealthOmics

Private workflows

Before you create and run a private workflow, you need the following resources:

  • Genomics data stored in an Amazon S3 bucket or a HealthOmics sequence store.

  • An Amazon S3 bucket for the workflow outputs.

  • A workflow definition file (in WDL, Nextflow, or CWL).

  • An Amazon ECR container image stored in a private Amazon ECR repository.

HealthOmics supports workflows written in WDL versions 1.0 and 1.1, Nextflow v22.04.0, or CWL versions 1.0, 1.1, or 1.2. To learn more about workflow languages, see the specifications for WDL, Nextflow, or CWL.

To use a private workflow, you containerize your workflow tools and create corresponding private image repositories in Amazon Elastic Container Registry (Amazon ECR). We recommend that you define your Amazon ECR container image URIs as parameters in your workflow so that access can be verified before the run begins. It also makes it easier to run a workflow in a new Region by changing the Region parameter.

Using the HealthOmics console or API operations, you can perform the following actions related to private workflows:

  • Create, retrieve, and manage workflows

  • Create and manage run groups

  • Share your private workflow with other AWS accounts in the same region, and accept private workflow shares offered to you by other AWS accounts

  • Tag AWS resources such as workflows, runs, and run groups

For full examples of how to use HealthOmics workflows, see HealthOmics Github tutorials or the AWS workshop end to end tutorial for HealthOmics.

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