HealthOmics Workflows - AWS HealthOmics

HealthOmics Workflows

With HealthOmics Workflows, you can process and analyze your genomics data using either Ready2Run workflows or private workflows described in CWL, WDL, or Nextflow that you create yourself.

Ready2Run workflows are created by life science publishers. They are ready to run without further definition or configuration. Private workflows are created and defined by you. A run is a single invocation of a workflow, and a task is a single process within the run.

HealthOmics workflows use your requested vCPU and memory to run each task. Before you create a workflow, you must containerize your workflow tools and create corresponding private image repositories in Amazon Elastic Container Registry (Amazon ECR). You can run a workflow on genomics data that's stored in an Amazon S3 bucket or in an HealthOmics sequence store.

With the workflow API operations, you can perform the following actions:

  • Creating, retrieving, and managing workflows

  • Starting and managing runs, including cancellation and deletion

  • Tracking the status of ongoing runs

  • Creating and managing run groups

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

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

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