Task resources in a HealthOmics workflow definition

In the workflow definition, define the following for each task:

• The container image for task. For more information, see Container images for private workflows.

• The number of CPUs and memory required for the task. For more information, see Compute and memory requirements for HealthOmics tasks.

• The optional per-task ephemeral storage that the task can use at /tmp when enabled for the run. For more information, see Ephemeral storage for HealthOmics workflow tasks.

HealthOmics provides run storage that all tasks in the run can access. For more information, see Run storage types in HealthOmics workflows.

WDL

task my_task {
   runtime {
      container: "<aws-account-id>.dkr.ecr.<aws-region>.amazonaws.com/<image-name>"
      cpu: 2
      memory: "4 GB"
      disks: "100 GiB"                 # optional
   }
   ...
}          

For a WDL workflow, HealthOmics attempts up to two retries for a task that fails because of service errors (API request returns a 5XX HTTP status code). For more information about task retries, see Task Retries.

You can opt out of the retry behavior by specifying the following configuration for the task in the WDL definition file:

runtime {
   preemptible: 0
}           

NextFlow

process my_task {
   container "<aws-account-id>.dkr.ecr.<aws-region>.amazonaws.com/<image-name>"
   cpus 2
   memory "4 GiB"
   disk '100 GB'                       // optional
   ...
}          

CWL

cwlVersion: v1.2
class: CommandLineTool
requirements:
    DockerRequirement:
        dockerPull: "<aws-account-id>.dkr.ecr.<aws-region>.amazonaws.com/<image-name>"
    ResourceRequirement:
        coresMax: 2
        ramMax: 4000 # specified in mebibytes
        tmpdirMin: 102400 # 100 gibibytes expressed in mebibytes