AWS::Omics::Workflow - AWS CloudFormation
SyntaxPropertiesReturn values

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AWS::Omics::Workflow

Creates a private workflow. Before you create a private workflow, you must create and configure these required resources:

  • 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 AWS HealthOmics.

  • (Optional) Parameter template file: A parameter template file written in JSON. Create the file to define the run parameters, or AWS HealthOmics generates the parameter template for you. For more information, see Parameter template files for HealthOmics workflows.

  • ECR container images: Create container images for the workflow in a private ECR repository, or synchronize images from a supported upstream registry with your Amazon ECR private repository.

  • (Optional) Sentieon licenses: Request a Sentieon license to use the Sentieon software in private workflows.

For more information, see Creating or updating a private workflow in AWS HealthOmics in the AWS HealthOmics User Guide.

Syntax

To declare this entity in your AWS CloudFormation template, use the following syntax:

JSON

{
  "Type" : "AWS::Omics::Workflow",
  "Properties" : {
      "Accelerators" : String,
      "ContainerRegistryMap" : ContainerRegistryMap,
      "ContainerRegistryMapUri" : String,
      "DefinitionRepository" : DefinitionRepository,
      "DefinitionUri" : String,
      "Description" : String,
      "Engine" : String,
      "Main" : String,
      "Name" : String,
      "ParameterTemplate" : {Key: Value, ...},
      "ParameterTemplatePath" : String,
      "readmeMarkdown" : String,
      "readmePath" : String,
      "readmeUri" : String,
      "StorageCapacity" : Number,
      "StorageType" : String,
      "Tags" : {Key: Value, ...},
      "WorkflowBucketOwnerId" : String
    }
}

YAML

Type: AWS::Omics::Workflow
Properties:
  Accelerators: String
  ContainerRegistryMap: 
    ContainerRegistryMap
  ContainerRegistryMapUri: String
  DefinitionRepository: 
    DefinitionRepository
  DefinitionUri: String
  Description: String
  Engine: String
  Main: String
  Name: String
  ParameterTemplate: 
    Key: Value
  ParameterTemplatePath: String
  readmeMarkdown: String
  readmePath: String
  readmeUri: String
  StorageCapacity: Number
  StorageType: String
  Tags: 
    Key: Value
  WorkflowBucketOwnerId: String

Properties

Accelerators

Property description not available.

Required: No

Type: String

Allowed values: GPU

Minimum: 1

Maximum: 64

Update requires: Replacement

ContainerRegistryMap

Use a container registry map to specify mappings between the ECR private repository and one or more upstream registries. For more information, see Container images in the AWS HealthOmics User Guide.

Required: No

Type: ContainerRegistryMap

Update requires: Replacement

ContainerRegistryMapUri

Property description not available.

Required: No

Type: String

Pattern: ^[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+$

Minimum: 1

Maximum: 750

Update requires: Replacement

DefinitionRepository

Contains information about a source code repository that hosts the workflow definition files.

Required: No

Type: DefinitionRepository

Update requires: Replacement

DefinitionUri

The URI of a definition for the workflow.

Required: No

Type: String

Pattern: ^[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+$

Minimum: 1

Maximum: 256

Update requires: Replacement

Description

The parameter's description.

Required: No

Type: String

Pattern: ^[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+$

Minimum: 1

Maximum: 256

Update requires: No interruption

Engine

An engine for the workflow.

Required: No

Type: String

Allowed values: WDL | NEXTFLOW | CWL

Minimum: 1

Maximum: 64

Update requires: Replacement

Main

The path of the main definition file for the workflow.

Required: No

Type: String

Pattern: ^[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+$

Minimum: 1

Maximum: 128

Update requires: Replacement

Name

The workflow's name.

Required: No

Type: String

Pattern: ^[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+$

Minimum: 1

Maximum: 128

Update requires: No interruption

ParameterTemplate

The workflow's parameter template.

Required: No

Type: Object of WorkflowParameter

Update requires: Replacement

ParameterTemplatePath

Property description not available.

Required: No

Type: String

Pattern: ^[\S]+$

Update requires: Replacement

readmeMarkdown

Property description not available.

Required: No

Type: String

Update requires: No interruption

readmePath

Property description not available.

Required: No

Type: String

Pattern: ^[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+$

Minimum: 1

Maximum: 128

Update requires: Replacement

readmeUri

Property description not available.

Required: No

Type: String

Pattern: ^s3://([a-z0-9][a-z0-9-.]{1,61}[a-z0-9])/((.{1,1024}))$

Update requires: Replacement

StorageCapacity

The default static storage capacity (in gibibytes) for runs that use this workflow or workflow version. The storageCapacity can be overwritten at run time. The storage capacity is not required for runs with a DYNAMIC storage type.

Required: No

Type: Number

Minimum: 0

Maximum: 100000

Update requires: Replacement

StorageType

Property description not available.

Required: No

Type: String

Allowed values: STATIC | DYNAMIC

Minimum: 1

Maximum: 64

Update requires: No interruption

Tags

Tags for the workflow.

Required: No

Type: Object of String

Pattern: .+

Minimum: 0

Maximum: 256

Update requires: No interruption

WorkflowBucketOwnerId

Property description not available.

Required: No

Type: String

Pattern: ^[0-9]{12}$

Update requires: Replacement

Return values

Ref

When you pass the logical ID of this resource to the intrinsic Ref function, Ref returns the details of this resource. For example:

{ "Ref": "Workflow.Type" }Ref returns the type of workflow.

Fn::GetAtt

The Fn::GetAtt intrinsic function returns a value for a specified attribute of this type. The following are the available attributes and sample return values.

For more information about using the Fn::GetAtt intrinsic function, see Fn::GetAtt.

Arn

The ARN for the workflow.

CreationTime

When the workflow was created.

Id

The workflow's ID.

Status

The workflow's status.

Type

The workflow's type.

Uuid

Property description not available.