2025/07/24 - Amazon Omics - 6 updated api methods
Changes Add Git integration and README support for HealthOmics workflows
{'definitionRepository': {'connectionArn': 'string',
'excludeFilePatterns': ['string'],
'fullRepositoryId': 'string',
'sourceReference': {'type': 'BRANCH | TAG | COMMIT',
'value': 'string'}},
'parameterTemplatePath': 'string',
'readmeMarkdown': 'string',
'readmePath': 'string',
'readmeUri': 'string',
'workflowBucketOwnerId': 'string'}
Creates a private workflow. Before you create a private workflow, you must create and configure these required resources:
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. The workflow definition file must be in .zip format.
(Optional) Parameter template: You can create a parameter template file that defines the run parameters, or Amazon Web Services HealthOmics can generate the parameter template for you.
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 using the Sentieon software in a private workflow.
For more information, see Creating or updating a private workflow in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.
See also: AWS API Documentation
Request Syntax
client.create_workflow(
name='string',
description='string',
engine='WDL'|'NEXTFLOW'|'CWL',
definitionZip=b'bytes',
definitionUri='string',
main='string',
parameterTemplate={
'string': {
'description': 'string',
'optional': True|False
}
},
storageCapacity=123,
tags={
'string': 'string'
},
requestId='string',
accelerators='GPU',
storageType='STATIC'|'DYNAMIC',
readmeMarkdown='string',
parameterTemplatePath='string',
readmePath='string',
definitionRepository={
'connectionArn': 'string',
'fullRepositoryId': 'string',
'sourceReference': {
'type': 'BRANCH'|'TAG'|'COMMIT',
'value': 'string'
},
'excludeFilePatterns': [
'string',
]
},
workflowBucketOwnerId='string',
readmeUri='string'
)
string
Name (optional but highly recommended) for the workflow to locate relevant information in the CloudWatch logs and Amazon Web Services HealthOmics console.
string
A description for the workflow.
string
The workflow engine for the workflow. This is only required if you have workflow definition files from more than one engine in your zip file. Otherwise, the service can detect the engine automatically from your workflow definition.
bytes
A ZIP archive containing the main workflow definition file and dependencies that it imports for the workflow. You can use a file with a ://fileb prefix instead of the Base64 string. For more information, see Workflow definition requirements in the Amazon Web Services HealthOmics User Guide.
string
The S3 URI of a definition for the workflow. The S3 bucket must be in the same region as the workflow.
string
The path of the main definition file for the workflow. This parameter is not required if the ZIP archive contains only one workflow definition file, or if the main definition file is named “main”. An example path is: workflow-definition/main-file.wdl.
dict
A parameter template for the workflow. If this field is blank, Amazon Web Services HealthOmics will automatically parse the parameter template values from your workflow definition file. To override these service generated default values, provide a parameter template. To view an example of a parameter template, see Parameter template files in the Amazon Web Services HealthOmics User Guide.
(string) --
(dict) --
A workflow parameter.
description (string) --
The parameter's description.
optional (boolean) --
Whether the parameter is optional.
integer
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.
dict
Tags for the workflow. You can define up to 50 tags for the workflow. For more information, see Adding a tag in the Amazon Web Services HealthOmics User Guide.
(string) --
(string) --
string
[REQUIRED]
An idempotency token to ensure that duplicate workflows are not created when Amazon Web Services HealthOmics submits retry requests.
This field is autopopulated if not provided.
string
The computational accelerator specified to run the workflow.
string
The default storage type for runs that use this workflow. The storageType can be overridden at run time. DYNAMIC storage dynamically scales the storage up or down, based on file system utilization. STATIC storage allocates a fixed amount of storage. For more information about dynamic and static storage types, see Run storage types in the Amazon Web Services HealthOmics User Guide.
string
The markdown content for the workflow's README file. This provides documentation and usage information for users of the workflow.
string
The path to the workflow parameter template JSON file within the repository. This file defines the input parameters for runs that use this workflow. If not specified, the workflow will be created without a parameter template.
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.
dict
The repository information for the workflow definition. This allows you to source your workflow definition directly from a code repository.
connectionArn (string) -- [REQUIRED]
The Amazon Resource Name (ARN) of the connection to the source code repository.
fullRepositoryId (string) -- [REQUIRED]
The full repository identifier, including the repository owner and name. For example, 'repository-owner/repository-name'.
sourceReference (dict) --
The source reference for the repository, such as a branch name, tag, or commit ID.
type (string) -- [REQUIRED]
The type of source reference, such as branch, tag, or commit.
value (string) -- [REQUIRED]
The value of the source reference, such as the branch name, tag name, or commit ID.
excludeFilePatterns (list) --
A list of file patterns to exclude when retrieving the workflow definition from the repository.
(string) --
string
The Amazon Web Services account ID of the expected owner of the S3 bucket that contains the workflow definition. If not specified, the service skips the validation.
string
The S3 URI of the README file for the workflow. This file provides documentation and usage information for the workflow. Requirements include:
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.
dict
Response Syntax
{
'arn': 'string',
'id': 'string',
'status': 'CREATING'|'ACTIVE'|'UPDATING'|'DELETED'|'FAILED'|'INACTIVE',
'tags': {
'string': 'string'
},
'uuid': 'string'
}
Response Structure
(dict) --
arn (string) --
The workflow's ARN.
id (string) --
The workflow's ID.
status (string) --
The workflow's status.
tags (dict) --
The workflow's tags.
(string) --
(string) --
uuid (string) --
The universally unique identifier (UUID) value for this workflow.
{'definitionRepository': {'connectionArn': 'string',
'excludeFilePatterns': ['string'],
'fullRepositoryId': 'string',
'sourceReference': {'type': 'BRANCH | TAG | COMMIT',
'value': 'string'}},
'parameterTemplatePath': 'string',
'readmeMarkdown': 'string',
'readmePath': 'string',
'readmeUri': 'string'}
Creates a new workflow version for the workflow that you specify with the workflowId parameter.
When you create a new version of a workflow, you need to specify the configuration for the new version. It doesn't inherit any configuration values from the workflow.
Provide a version name that is unique for this workflow. You cannot change the name after HealthOmics creates the version.
For more information, see Workflow versioning in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.
See also: AWS API Documentation
Request Syntax
client.create_workflow_version(
workflowId='string',
versionName='string',
definitionZip=b'bytes',
definitionUri='string',
accelerators='GPU',
description='string',
engine='WDL'|'NEXTFLOW'|'CWL',
main='string',
parameterTemplate={
'string': {
'description': 'string',
'optional': True|False
}
},
requestId='string',
storageType='STATIC'|'DYNAMIC',
storageCapacity=123,
tags={
'string': 'string'
},
workflowBucketOwnerId='string',
readmeMarkdown='string',
parameterTemplatePath='string',
readmePath='string',
definitionRepository={
'connectionArn': 'string',
'fullRepositoryId': 'string',
'sourceReference': {
'type': 'BRANCH'|'TAG'|'COMMIT',
'value': 'string'
},
'excludeFilePatterns': [
'string',
]
},
readmeUri='string'
)
string
[REQUIRED]
The ID of the workflow where you are creating the new version.
string
[REQUIRED]
A name for the workflow version. Provide a version name that is unique for this workflow. You cannot change the name after HealthOmics creates the version.
The version name must start with a letter or number and it can include upper-case and lower-case letters, numbers, hyphens, periods and underscores. The maximum length is 64 characters. You can use a simple naming scheme, such as version1, version2, version3. You can also match your workflow versions with your own internal versioning conventions, such as 2.7.0, 2.7.1, 2.7.2.
bytes
A zip archive containing the workflow definition for this workflow version.
string
The URI specifies the location of the workflow definition for this workflow version.
string
The computational accelerator for this workflow version.
string
A description for this workflow version.
string
The workflow engine for this workflow version.
string
The path of the main definition file for this workflow version.
dict
The parameter template defines the input parameters for runs that use this workflow version.
(string) --
(dict) --
A workflow parameter.
description (string) --
The parameter's description.
optional (boolean) --
Whether the parameter is optional.
string
[REQUIRED]
To ensure that requests don't run multiple times, specify a unique ID for each request.
This field is autopopulated if not provided.
string
The default storage type for runs that use this workflow. STATIC storage allocates a fixed amount of storage. DYNAMIC storage dynamically scales the storage up or down, based on file system utilization. For more information about static and dynamic storage, see Running workflows in the Amazon Web Services HealthOmics User Guide.
integer
The default static storage capacity (in gibibytes) for runs that use this workflow or workflow version.
dict
Optional tags to associate with this workflow version.
(string) --
(string) --
string
Amazon Web Services Id of the owner of the S3 bucket that contains the workflow definition. You need to specify this parameter if your account is not the bucket owner.
string
The markdown content for the workflow version's README file. This provides documentation and usage information for users of this specific workflow version.
string
The path to the workflow version parameter template JSON file within the repository. This file defines the input parameters for runs that use this workflow version. If not specified, the workflow version will be created without a parameter template.
string
The path to the workflow version 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.
dict
The repository information for the workflow version definition. This allows you to source your workflow version definition directly from a code repository.
connectionArn (string) -- [REQUIRED]
The Amazon Resource Name (ARN) of the connection to the source code repository.
fullRepositoryId (string) -- [REQUIRED]
The full repository identifier, including the repository owner and name. For example, 'repository-owner/repository-name'.
sourceReference (dict) --
The source reference for the repository, such as a branch name, tag, or commit ID.
type (string) -- [REQUIRED]
The type of source reference, such as branch, tag, or commit.
value (string) -- [REQUIRED]
The value of the source reference, such as the branch name, tag name, or commit ID.
excludeFilePatterns (list) --
A list of file patterns to exclude when retrieving the workflow definition from the repository.
(string) --
string
The S3 URI of the README file for the workflow version. This file provides documentation and usage information for the workflow version. Requirements include:
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.
dict
Response Syntax
{
'arn': 'string',
'workflowId': 'string',
'versionName': 'string',
'status': 'CREATING'|'ACTIVE'|'UPDATING'|'DELETED'|'FAILED'|'INACTIVE',
'tags': {
'string': 'string'
},
'uuid': 'string'
}
Response Structure
(dict) --
arn (string) --
ARN of the workflow version.
workflowId (string) --
The workflow's ID.
versionName (string) --
The workflow version name.
status (string) --
The workflow version status.
tags (dict) --
The workflow version's tags.
(string) --
(string) --
uuid (string) --
The universally unique identifier (UUID) value for this workflow version.
{'export': {'README'}}
Response {'definitionRepositoryDetails': {'connectionArn': 'string',
'fullRepositoryId': 'string',
'providerEndpoint': 'string',
'providerType': 'string',
'sourceReference': {'type': 'BRANCH | TAG | '
'COMMIT',
'value': 'string'}},
'readme': 'string',
'readmePath': 'string'}
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.
See also: AWS API Documentation
Request Syntax
client.get_workflow(
id='string',
type='PRIVATE'|'READY2RUN',
export=[
'DEFINITION'|'README',
],
workflowOwnerId='string'
)
string
[REQUIRED]
The workflow's ID.
string
The workflow's type.
list
The export format for the workflow.
(string) --
string
The ID of the workflow owner.
dict
Response Syntax
{
'arn': 'string',
'id': 'string',
'status': 'CREATING'|'ACTIVE'|'UPDATING'|'DELETED'|'FAILED'|'INACTIVE',
'type': 'PRIVATE'|'READY2RUN',
'name': 'string',
'description': 'string',
'engine': 'WDL'|'NEXTFLOW'|'CWL',
'definition': 'string',
'main': 'string',
'digest': 'string',
'parameterTemplate': {
'string': {
'description': 'string',
'optional': True|False
}
},
'storageCapacity': 123,
'creationTime': datetime(2015, 1, 1),
'statusMessage': 'string',
'tags': {
'string': 'string'
},
'metadata': {
'string': 'string'
},
'accelerators': 'GPU',
'storageType': 'STATIC'|'DYNAMIC',
'uuid': 'string',
'readme': 'string',
'definitionRepositoryDetails': {
'connectionArn': 'string',
'fullRepositoryId': 'string',
'sourceReference': {
'type': 'BRANCH'|'TAG'|'COMMIT',
'value': 'string'
},
'providerType': 'string',
'providerEndpoint': 'string'
},
'readmePath': 'string'
}
Response Structure
(dict) --
arn (string) --
The workflow's ARN.
id (string) --
The workflow's ID.
status (string) --
The workflow's status.
type (string) --
The workflow's type.
name (string) --
The workflow's name.
description (string) --
The workflow's description.
engine (string) --
The workflow's engine.
definition (string) --
The workflow's definition.
main (string) --
The path of the main definition file for the workflow.
digest (string) --
The workflow's digest.
parameterTemplate (dict) --
The workflow's parameter template.
(string) --
(dict) --
A workflow parameter.
description (string) --
The parameter's description.
optional (boolean) --
Whether the parameter is optional.
storageCapacity (integer) --
The default static storage capacity (in gibibytes) for runs that use this workflow or workflow version.
creationTime (datetime) --
When the workflow was created.
statusMessage (string) --
The workflow's status message.
tags (dict) --
The workflow's tags.
(string) --
(string) --
metadata (dict) --
Gets metadata for the workflow.
(string) --
(string) --
accelerators (string) --
The computational accelerator specified to run the workflow.
storageType (string) --
The default storage type for runs using this workflow.
uuid (string) --
The universally unique identifier (UUID) value for this workflow.
readme (string) --
The README content for the workflow, providing documentation and usage information.
definitionRepositoryDetails (dict) --
Details about the source code repository that hosts the workflow definition files.
connectionArn (string) --
The Amazon Resource Name (ARN) of the connection to the source code repository.
fullRepositoryId (string) --
The full repository identifier, including the repository owner and name. For example, 'repository-owner/repository-name'.
sourceReference (dict) --
The source reference for the repository, such as a branch name, tag, or commit ID.
type (string) --
The type of source reference, such as branch, tag, or commit.
value (string) --
The value of the source reference, such as the branch name, tag name, or commit ID.
providerType (string) --
The provider type of the source code repository, such as Bitbucket, GitHub, GitHubEnterpriseServer, GitLab, and GitLabSelfManaged.
providerEndpoint (string) --
The endpoint URL of the source code repository provider.
readmePath (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.
{'export': {'README'}}
Response {'definitionRepositoryDetails': {'connectionArn': 'string',
'fullRepositoryId': 'string',
'providerEndpoint': 'string',
'providerType': 'string',
'sourceReference': {'type': 'BRANCH | TAG | '
'COMMIT',
'value': 'string'}},
'readme': 'string',
'readmePath': 'string'}
Gets information about a workflow version. For more information, see Workflow versioning in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.
See also: AWS API Documentation
Request Syntax
client.get_workflow_version(
workflowId='string',
versionName='string',
type='PRIVATE'|'READY2RUN',
export=[
'DEFINITION'|'README',
],
workflowOwnerId='string'
)
string
[REQUIRED]
The workflow's ID.
string
[REQUIRED]
The workflow version name.
string
The workflow's type.
list
The export format for the workflow.
(string) --
string
Amazon Web Services Id of the owner of the workflow.
dict
Response Syntax
{
'arn': 'string',
'workflowId': 'string',
'versionName': 'string',
'accelerators': 'GPU',
'creationTime': datetime(2015, 1, 1),
'description': 'string',
'definition': 'string',
'digest': 'string',
'engine': 'WDL'|'NEXTFLOW'|'CWL',
'main': 'string',
'metadata': {
'string': 'string'
},
'parameterTemplate': {
'string': {
'description': 'string',
'optional': True|False
}
},
'status': 'CREATING'|'ACTIVE'|'UPDATING'|'DELETED'|'FAILED'|'INACTIVE',
'statusMessage': 'string',
'storageType': 'STATIC'|'DYNAMIC',
'storageCapacity': 123,
'type': 'PRIVATE'|'READY2RUN',
'tags': {
'string': 'string'
},
'uuid': 'string',
'workflowBucketOwnerId': 'string',
'readme': 'string',
'definitionRepositoryDetails': {
'connectionArn': 'string',
'fullRepositoryId': 'string',
'sourceReference': {
'type': 'BRANCH'|'TAG'|'COMMIT',
'value': 'string'
},
'providerType': 'string',
'providerEndpoint': 'string'
},
'readmePath': 'string'
}
Response Structure
(dict) --
arn (string) --
ARN of the workflow version.
workflowId (string) --
The workflow's ID.
versionName (string) --
The workflow version name.
accelerators (string) --
The accelerator for this workflow version.
creationTime (datetime) --
When the workflow version was created.
description (string) --
Description of the workflow version.
definition (string) --
Definition of the workflow version.
digest (string) --
The workflow version's digest.
engine (string) --
The workflow engine for this workflow version.
main (string) --
The path of the main definition file for the workflow.
metadata (dict) --
The metadata for the workflow version.
(string) --
(string) --
parameterTemplate (dict) --
The parameter template for the workflow version.
(string) --
(dict) --
A workflow parameter.
description (string) --
The parameter's description.
optional (boolean) --
Whether the parameter is optional.
status (string) --
The workflow version status
statusMessage (string) --
The workflow version status message
storageType (string) --
The default storage type for the run.
storageCapacity (integer) --
The default run storage capacity for static storage.
type (string) --
The workflow version type
tags (dict) --
The workflow version tags
(string) --
(string) --
uuid (string) --
The universally unique identifier (UUID) value for this workflow version
workflowBucketOwnerId (string) --
Amazon Web Services Id of the owner of the bucket.
readme (string) --
The README content for the workflow version, providing documentation and usage information specific to this version.
definitionRepositoryDetails (dict) --
Details about the source code repository that hosts the workflow version definition files.
connectionArn (string) --
The Amazon Resource Name (ARN) of the connection to the source code repository.
fullRepositoryId (string) --
The full repository identifier, including the repository owner and name. For example, 'repository-owner/repository-name'.
sourceReference (dict) --
The source reference for the repository, such as a branch name, tag, or commit ID.
type (string) --
The type of source reference, such as branch, tag, or commit.
value (string) --
The value of the source reference, such as the branch name, tag name, or commit ID.
providerType (string) --
The provider type of the source code repository, such as Bitbucket, GitHub, GitHubEnterpriseServer, GitLab, and GitLabSelfManaged.
providerEndpoint (string) --
The endpoint URL of the source code repository provider.
readmePath (string) --
The path to the workflow version 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.
{'readmeMarkdown': 'string'}
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.
See also: AWS API Documentation
Request Syntax
client.update_workflow(
id='string',
name='string',
description='string',
storageType='STATIC'|'DYNAMIC',
storageCapacity=123,
readmeMarkdown='string'
)
string
[REQUIRED]
The workflow's ID.
string
A name for the workflow.
string
A description for the workflow.
string
The default storage type for runs that use this workflow. STATIC storage allocates a fixed amount of storage. DYNAMIC storage dynamically scales the storage up or down, based on file system utilization. For more information about static and dynamic storage, see Running workflows in the Amazon Web Services HealthOmics User Guide.
integer
The default static storage capacity (in gibibytes) for runs that use this workflow or workflow version.
string
The markdown content for the workflow's README file. This provides documentation and usage information for users of the workflow.
None
{'readmeMarkdown': 'string'}
Updates information about the workflow version. For more information, see Workflow versioning in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide.
See also: AWS API Documentation
Request Syntax
client.update_workflow_version(
workflowId='string',
versionName='string',
description='string',
storageType='STATIC'|'DYNAMIC',
storageCapacity=123,
readmeMarkdown='string'
)
string
[REQUIRED]
The workflow's ID.
string
[REQUIRED]
The name of the workflow version.
string
Description of the workflow version.
string
The default storage type for runs that use this workflow. STATIC storage allocates a fixed amount of storage. DYNAMIC storage dynamically scales the storage up or down, based on file system utilization. For more information about static and dynamic storage, see Running workflows in the Amazon Web Services HealthOmics User Guide.
integer
The default static storage capacity (in gibibytes) for runs that use this workflow or workflow version.
string
The markdown content for the workflow version's README file. This provides documentation and usage information for users of this specific workflow version.
None