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Task resources in a HealthOmics workflow definition

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Task resources in a HealthOmics workflow definition - AWS HealthOmics

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

HealthOmics ignores any per-task storage specifications. 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"
   }
   ...
}

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

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
}
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