AWS::Omics::Workflow - AWS CloudFormation (original) (raw)

Creates a private workflow.Private workflows depend on a variety of resources that you create and configure before creating the workflow:

• Input data: Input data for the workflow, stored in an S3 bucket or a AWS HealthOmics sequence store.
• Workflow definition files: Define your workflow in one or more workflow definition files, 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.
• Parameter template files: Define run parameters using a parameter template file (written in JSON).
• ECR container images: Create one or more container images for the workflow. Store the images in a private ECR repository.
• (Optional) Sentieon licenses: Request a Sentieon license if you plan to use Sentieon software in a private workflow.

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,
      "DefinitionUri" : String,
      "Description" : String,
      "Engine" : String,
      "Main" : String,
      "Name" : String,
      "ParameterTemplate" : {Key: Value, ...},
      "StorageCapacity" : Number,
      "Tags" : {Key: Value, ...}
    }
}

YAML

Type: AWS::Omics::Workflow
Properties:
  Accelerators: String
  DefinitionUri: String
  Description: String
  Engine: String
  Main: String
  Name: String
  ParameterTemplate: 
    Key: Value
  StorageCapacity: Number
  Tags: 
    Key: Value

Properties

Accelerators

Property description not available.

Required: No

Type: String

Allowed values: GPU

Minimum: 1

Maximum: 64

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

StorageCapacity

The default static storage capacity (in gibibytes) for runs that use this workflow or workflow version.

Required: No

Type: Number

Minimum: 0

Maximum: 100000

Update requires: Replacement

Tags

Tags for the workflow.

Required: No

Type: Object of String

Pattern: .+

Minimum: 0

Maximum: 256

Update requires: No interruption

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.