workflows

Creates, updates, deletes or gets a workflow resource or lists workflows in a region

Overview

Name	workflows
Type	Resource
Description	Definition of AWS::Omics::Workflow Resource Type
Id	awscc.omics.workflows

Fields

get (all properties)

Name	Datatype	Description
arn	string
creation_time	string
definition_uri	string
description	string
engine	string
id	string
main	string
name	string
parameter_template	object
status	string
accelerators	string
storage_capacity	number
tags	object	A map of resource tags
type	string
storage_type	string
uuid	string
workflow_bucket_owner_id	string	Optional workflow bucket owner ID to verify the workflow bucket
▶definition_repository	object
parameter_template_path	string	Path to the primary workflow parameter template JSON file inside the repository
readme_path	string	The path to the workflow README markdown file within the repository. This file provides documentation and usage information for the workflow. If not specified, the README.md file from the root directory of the repository will be used.
readme_uri	string	The S3 URI of the README file for the workflow. This file provides documentation and usage information for the workflow. The S3 URI must begin with s3://USER-OWNED-BUCKET/. The requester must have access to the S3 bucket and object. The max README content length is 500 KiB.
readme_markdown	string	The markdown content for the workflow's README file. This provides documentation and usage information for users of the workflow.
region	string	AWS region.

list (identifiers only)

Name	Datatype	Description
id	string
region	string	AWS region.

For more information, see AWS::Omics::Workflow.

Methods

Name	Resource	Accessible by	Required Params
create_resource	workflows	INSERT	region
delete_resource	workflows	DELETE	Identifier, region
update_resource	workflows	UPDATE	Identifier, PatchDocument, region
list_resources	workflows_list_only	SELECT	region
get_resource	workflows	SELECT	Identifier, region

SELECT examples

get (all properties)

Gets all properties from an individual workflow.

SELECT
  region,
  arn,
  creation_time,
  definition_uri,
  description,
  engine,
  id,
  main,
  name,
  parameter_template,
  status,
  accelerators,
  storage_capacity,
  tags,
  type,
  storage_type,
  uuid,
  workflow_bucket_owner_id,
  definition_repository,
  parameter_template_path,
  readme_path,
  readme_uri,
  readme_markdown
FROM awscc.omics.workflows
WHERE
  region = 'us-east-1' AND
  Identifier = '{{ id }}';

list (identifiers only)

Lists all workflows in a region.

SELECT
  region,
  id
FROM awscc.omics.workflows_list_only
WHERE
  region = 'us-east-1';

INSERT example

Use the following StackQL query and manifest file to create a new workflow resource, using stack-deploy.

Required Properties

/*+ create */
INSERT INTO awscc.omics.workflows (
  DefinitionUri,
  Description,
  Engine,
  Main,
  Name,
  ParameterTemplate,
  Accelerators,
  StorageCapacity,
  Tags,
  StorageType,
  WorkflowBucketOwnerId,
  DefinitionRepository,
  ParameterTemplatePath,
  readmePath,
  readmeUri,
  readmeMarkdown,
  region
)
SELECT
  '{{ definition_uri }}',
  '{{ description }}',
  '{{ engine }}',
  '{{ main }}',
  '{{ name }}',
  '{{ parameter_template }}',
  '{{ accelerators }}',
  '{{ storage_capacity }}',
  '{{ tags }}',
  '{{ storage_type }}',
  '{{ workflow_bucket_owner_id }}',
  '{{ definition_repository }}',
  '{{ parameter_template_path }}',
  '{{ readme_path }}',
  '{{ readme_uri }}',
  '{{ readme_markdown }}',
  '{{ region }}';

All Properties

/*+ create */
INSERT INTO awscc.omics.workflows (
  DefinitionUri,
  Description,
  Engine,
  Main,
  Name,
  ParameterTemplate,
  Accelerators,
  StorageCapacity,
  Tags,
  StorageType,
  WorkflowBucketOwnerId,
  DefinitionRepository,
  ParameterTemplatePath,
  readmePath,
  readmeUri,
  readmeMarkdown,
  region
)
SELECT
  '{{ definition_uri }}',
  '{{ description }}',
  '{{ engine }}',
  '{{ main }}',
  '{{ name }}',
  '{{ parameter_template }}',
  '{{ accelerators }}',
  '{{ storage_capacity }}',
  '{{ tags }}',
  '{{ storage_type }}',
  '{{ workflow_bucket_owner_id }}',
  '{{ definition_repository }}',
  '{{ parameter_template_path }}',
  '{{ readme_path }}',
  '{{ readme_uri }}',
  '{{ readme_markdown }}',
  '{{ region }}';

Manifest

version: 1
name: stack name
description: stack description
providers:
  - aws
globals:
  - name: region
    value: '{{ vars.AWS_REGION }}'
resources:
  - name: workflow
    props:
      - name: definition_uri
        value: '{{ definition_uri }}'
      - name: description
        value: '{{ description }}'
      - name: engine
        value: '{{ engine }}'
      - name: main
        value: '{{ main }}'
      - name: name
        value: '{{ name }}'
      - name: parameter_template
        value: {}
      - name: accelerators
        value: '{{ accelerators }}'
      - name: storage_capacity
        value: null
      - name: tags
        value: {}
      - name: storage_type
        value: '{{ storage_type }}'
      - name: workflow_bucket_owner_id
        value: '{{ workflow_bucket_owner_id }}'
      - name: definition_repository
        value:
          connection_arn: '{{ connection_arn }}'
          full_repository_id: '{{ full_repository_id }}'
          source_reference:
            type: '{{ type }}'
            value: '{{ value }}'
          exclude_file_patterns:
            - '{{ exclude_file_patterns[0] }}'
      - name: parameter_template_path
        value: '{{ parameter_template_path }}'
      - name: readme_path
        value: '{{ readme_path }}'
      - name: readme_uri
        value: '{{ readme_uri }}'
      - name: readme_markdown
        value: '{{ readme_markdown }}'

UPDATE example

Use the following StackQL query and manifest file to update a workflow resource, using stack-deploy.

/*+ update */
UPDATE awscc.omics.workflows
SET PatchDocument = string('{{ {
    "Description": description,
    "Name": name,
    "Tags": tags,
    "StorageType": storage_type,
    "readmeMarkdown": readme_markdown
} | generate_patch_document }}')
WHERE
  region = '{{ region }}' AND
  Identifier = '{{ id }}';

DELETE example

/*+ delete */
DELETE FROM awscc.omics.workflows
WHERE
  Identifier = '{{ id }}' AND
  region = 'us-east-1';

Permissions

To operate on the workflows resource, the following permissions are required:

Create

omics:CreateWorkflow,
omics:GetWorkflow,
omics:TagResource,
s3:PutObject,
s3:GetObject,
s3:GetObjectAttributes,
s3:HeadObject,
s3:GetEncryptionConfiguration,
kms:Decrypt,
kms:GenerateDataKey,
kms:GenerateDataKeyPair,
kms:GenerateDataKeyPairWithoutPlaintext,
kms:GenerateDataKeyWithoutPlaintext,
codeconnections:UseConnection,
codeconnections:GetConnection,
codeconnections:GetHost

Read

omics:GetWorkflow

Update

omics:UpdateWorkflow,
omics:GetWorkflow,
omics:TagResource,
omics:ListTagsForResource,
omics:UntagResource

Delete

omics:DeleteWorkflow,
omics:GetWorkflow

List

omics:ListWorkflows