workflows

Creates, updates, deletes, gets or lists a workflows resource.

Overview

Name	workflows
Type	Resource
Id	aws.omics.workflows

Fields

The following fields are returned by SELECT queries:

get_workflow

Name	Datatype	Description
id	string	The workflow's ID. (pattern: <code>[0-9]+</code>)
name	string	The workflow's name. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
accelerators	string	The computational accelerator specified to run the workflow. (GPU)
arn	string	The workflow's ARN. (pattern: <code>arn:.+</code>)
container_registry_map	object	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 Amazon Web Services HealthOmics User Guide.
creation_time	string (date-time)	When the workflow was created.
definition	string	The workflow's definition. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
definition_repository_details	object	Details about the source code repository that hosts the workflow definition files.
description	string	The workflow's description. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
digest	string	The workflow's digest.
engine	string	The workflow's engine. (WDL, NEXTFLOW, CWL, WDL_LENIENT)
main	string	The path of the main definition file for the workflow. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
metadata	object	Gets metadata for the workflow.
parameter_template	object	The workflow's parameter template.
profile_parameter_templates	object	A mapping of profile names to their parameter templates. Each profile defines its own set of parameters that you can use when starting a run with that profile.
profiles	array	The list of Nextflow profiles that are available for this workflow. Profiles allow you to select predefined configuration settings at runtime.
readme	string	The README content for the workflow, providing documentation and usage information. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
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. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
status	string	The workflow's status. (CREATING, ACTIVE, UPDATING, DELETED, FAILED, INACTIVE)
status_message	string	The workflow's status message. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
storage_capacity	integer	The default static storage capacity (in gibibytes) for runs that use this workflow or workflow version.
storage_type	string	The default storage type for runs using this workflow. (STATIC, DYNAMIC)
tags	object	The workflow's tags.
type_	string	The workflow's type. (PRIVATE, READY2RUN)
uuid	string	The universally unique identifier (UUID) value for this workflow. (pattern: <code>[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}</code>)

list_workflows

Name	Datatype	Description
id	string	The workflow's ID. (pattern: <code>[0-9]+</code>)
name	string	The workflow's name. (pattern: <code>[\p{L}||\p{M}||\p{Z}||\p{S}||\p{N}||\p{P}]+</code>)
arn	string	The workflow's ARN. (pattern: <code>arn:.+</code>)
creation_time	string (date-time)	When the workflow was created.
digest	string	The workflow's digest.
metadata	object	Any metadata available for workflow. The information listed may vary depending on the workflow, and there may also be no metadata to return.
status	string	The workflow's status. (CREATING, ACTIVE, UPDATING, DELETED, FAILED, INACTIVE)
type_	string	The workflow's type. (PRIVATE, READY2RUN)

Methods

The following methods are available for this resource:

Name	Accessible by	Required Params	Optional Params	Description
get_workflow	select	id, region	type, export, workflowOwnerId	Gets all information about a workflow using its ID. If a workflow is shared with you, you cannot export the workflow. For more information about your workflow status, see Verify the workflow status in the Amazon Web Services HealthOmics User Guide.
list_workflows	select	region	type, name, startingToken, maxResults	Retrieves a list of existing workflows. You can filter for specific workflows by their name and type. Using the type parameter, specify PRIVATE to retrieve a list of private workflows or specify READY2RUN for a list of all Ready2Run workflows. If you do not specify the type of workflow, this operation returns a list of existing workflows.
create_workflow	insert	region, requestId		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 Amazon Web Services HealthOmics. You can use Amazon Q CLI to build and validate your workflow definition files in WDL, Nextflow, and CWL. For more information, see Example prompts for Amazon Q CLI and the Amazon Web Services HealthOmics Agentic generative AI tutorial on GitHub. (Optional) Parameter template file: A parameter template file written in JSON. Create the file to define the run parameters, or Amazon Web Services 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 Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.
update_workflow	update	id, region		Updates information about a workflow. You can update the following workflow information: Name Description Default storage type Default storage capacity (with workflow ID) This operation returns a response with no body if the operation is successful. You can check the workflow updates by calling the GetWorkflow API operation. For more information, see Update a private workflow in the Amazon Web Services HealthOmics User Guide.
delete_workflow	delete	id, region		Deletes a workflow by specifying its ID. This operation returns a response with no body if the deletion is successful. To verify that the workflow is deleted: Use ListWorkflows to confirm the workflow no longer appears in the list. Use GetWorkflow to verify the workflow cannot be found.

Parameters

Parameters can be passed in the WHERE clause of a query. Check the Methods section to see which parameters are required or optional for each operation.

Name	Datatype	Description
id	string	The workflow's ID.
region	string	AWS region (default: us-east-1)
export	array	The export format for the workflow.
maxResults	integer	The maximum number of workflows to return in one page of results.
name	string	Filter the list by workflow name.
startingToken	string	Specify the pagination token from a previous request to retrieve the next page of results.
type	string	Filter the list by workflow type.
workflowOwnerId	string	The ID of the workflow owner.

SELECT examples

get_workflow

Gets all information about a workflow using its ID. If a workflow is shared with you, you cannot export the workflow. For more information about your workflow status, see Verify the workflow status in the Amazon Web Services HealthOmics User Guide.

SELECT
id,
name,
accelerators,
arn,
container_registry_map,
creation_time,
definition,
definition_repository_details,
description,
digest,
engine,
main,
metadata,
parameter_template,
profile_parameter_templates,
profiles,
readme,
readme_path,
status,
status_message,
storage_capacity,
storage_type,
tags,
type_,
uuid
FROM aws.omics.workflows
WHERE id = '{{ id }}' -- required
AND region = '{{ region }}' -- required
AND type = '{{ type }}'
AND export = '{{ export }}'
AND workflowOwnerId = '{{ workflowOwnerId }}'
;

list_workflows

Retrieves a list of existing workflows. You can filter for specific workflows by their name and type. Using the type parameter, specify PRIVATE to retrieve a list of private workflows or specify READY2RUN for a list of all Ready2Run workflows. If you do not specify the type of workflow, this operation returns a list of existing workflows.

SELECT
id,
name,
arn,
creation_time,
digest,
metadata,
status,
type_
FROM aws.omics.workflows
WHERE region = '{{ region }}' -- required
AND type = '{{ type }}'
AND name = '{{ name }}'
AND startingToken = '{{ startingToken }}'
AND maxResults = '{{ maxResults }}'
;

INSERT examples

create_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 Amazon Web Services HealthOmics. You can use Amazon Q CLI to build and validate your workflow definition files in WDL, Nextflow, and CWL. For more information, see Example prompts for Amazon Q CLI and the Amazon Web Services HealthOmics Agentic generative AI tutorial on GitHub. (Optional) Parameter template file: A parameter template file written in JSON. Create the file to define the run parameters, or Amazon Web Services 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 Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.

INSERT INTO aws.omics.workflows (
name,
description,
engine,
definitionZip,
definitionUri,
main,
parameterTemplate,
storageCapacity,
tags,
requestId,
accelerators,
storageType,
containerRegistryMap,
containerRegistryMapUri,
readmeMarkdown,
parameterTemplatePath,
readmePath,
definitionRepository,
workflowBucketOwnerId,
readmeUri,
region
)
SELECT 
'{{ name }}',
'{{ description }}',
'{{ engine }}',
'{{ definitionZip }}',
'{{ definitionUri }}',
'{{ main }}',
'{{ parameterTemplate }}',
{{ storageCapacity }},
'{{ tags }}',
'{{ requestId }}' /* required */,
'{{ accelerators }}',
'{{ storageType }}',
'{{ containerRegistryMap }}',
'{{ containerRegistryMapUri }}',
'{{ readmeMarkdown }}',
'{{ parameterTemplatePath }}',
'{{ readmePath }}',
'{{ definitionRepository }}',
'{{ workflowBucketOwnerId }}',
'{{ readmeUri }}',
'{{ region }}'
RETURNING
id,
arn,
status,
tags,
uuid
;

Manifest

# Description fields are for documentation purposes
- name: workflows
props:
  - name: region
    value: "{{ region }}"
    description: Required parameter for the workflows resource.
  - name: name
    value: "{{ name }}"
  - name: description
    value: "{{ description }}"
  - name: engine
    value: "{{ engine }}"
    valid_values: ['WDL', 'NEXTFLOW', 'CWL', 'WDL_LENIENT']
  - name: definitionZip
    value: "{{ definitionZip }}"
  - name: definitionUri
    value: "{{ definitionUri }}"
  - name: main
    value: "{{ main }}"
  - name: parameterTemplate
    value: "{{ parameterTemplate }}"
  - name: storageCapacity
    value: {{ storageCapacity }}
  - name: tags
    value: "{{ tags }}"
  - name: requestId
    value: "{{ requestId }}"
  - name: accelerators
    value: "{{ accelerators }}"
    valid_values: ['GPU']
  - name: storageType
    value: "{{ storageType }}"
    valid_values: ['STATIC', 'DYNAMIC']
  - name: containerRegistryMap
    description: |
      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 Amazon Web Services HealthOmics User Guide.
    value:
      registryMappings:
        - upstreamRegistryUrl: "{{ upstreamRegistryUrl }}"
          ecrRepositoryPrefix: "{{ ecrRepositoryPrefix }}"
          upstreamRepositoryPrefix: "{{ upstreamRepositoryPrefix }}"
          ecrAccountId: "{{ ecrAccountId }}"
      imageMappings:
        - sourceImage: "{{ sourceImage }}"
          destinationImage: "{{ destinationImage }}"
  - name: containerRegistryMapUri
    value: "{{ containerRegistryMapUri }}"
  - name: readmeMarkdown
    value: "{{ readmeMarkdown }}"
  - name: parameterTemplatePath
    value: "{{ parameterTemplatePath }}"
  - name: readmePath
    value: "{{ readmePath }}"
  - name: definitionRepository
    description: |
      Contains information about a source code repository that hosts the workflow definition files.
    value:
      connectionArn: "{{ connectionArn }}"
      fullRepositoryId: "{{ fullRepositoryId }}"
      sourceReference:
        type_: "{{ type_ }}"
        value: "{{ value }}"
      excludeFilePatterns:
        - "{{ excludeFilePatterns }}"
  - name: workflowBucketOwnerId
    value: "{{ workflowBucketOwnerId }}"
  - name: readmeUri
    value: "{{ readmeUri }}"

UPDATE examples

update_workflow

Updates information about a workflow. You can update the following workflow information: Name Description Default storage type Default storage capacity (with workflow ID) This operation returns a response with no body if the operation is successful. You can check the workflow updates by calling the GetWorkflow API operation. For more information, see Update a private workflow in the Amazon Web Services HealthOmics User Guide.

UPDATE aws.omics.workflows
SET 
name = '{{ name }}',
description = '{{ description }}',
storageType = '{{ storageType }}',
storageCapacity = {{ storageCapacity }},
readmeMarkdown = '{{ readmeMarkdown }}'
WHERE 
id = '{{ id }}' --required
AND region = '{{ region }}' --required;

DELETE examples

delete_workflow

Deletes a workflow by specifying its ID. This operation returns a response with no body if the deletion is successful. To verify that the workflow is deleted: Use ListWorkflows to confirm the workflow no longer appears in the list. Use GetWorkflow to verify the workflow cannot be found.

DELETE FROM aws.omics.workflows
WHERE id = '{{ id }}' --required
AND region = '{{ region }}' --required
;