2025/04/17 - Amazon Omics - 5 new6 updated api methods
Changes Add versioning for HealthOmics workflows
Lists the workflow versions for the specified workflow. 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.list_workflow_versions( workflowId='string', type='PRIVATE'|'READY2RUN', workflowOwnerId='string', startingToken='string', maxResults=123 )
string
[REQUIRED]
The workflow's ID.
string
The workflow type.
string
Amazon Web Services Id of the owner of the workflow.
string
Specify the pagination token from a previous request to retrieve the next page of results.
integer
The maximum number of workflows to return in one page of results.
dict
Response Syntax
{ 'items': [ { 'arn': 'string', 'workflowId': 'string', 'versionName': 'string', 'description': 'string', 'status': 'CREATING'|'ACTIVE'|'UPDATING'|'DELETED'|'FAILED'|'INACTIVE', 'type': 'PRIVATE'|'READY2RUN', 'digest': 'string', 'creationTime': datetime(2015, 1, 1), 'metadata': { 'string': 'string' } }, ], 'nextToken': 'string' }
Response Structure
(dict) --
items (list) --
A list of workflow version items.
(dict) --
A list of workflow version items.
arn (string) --
ARN of the workflow version.
workflowId (string) --
The workflow's ID.
versionName (string) --
The name of the workflow version.
description (string) --
The description of the workflow version.
status (string) --
The status of the workflow version.
type (string) --
The type of the workflow version.
digest (string) --
The digist of the workflow version.
creationTime (datetime) --
The creation time of the workflow version.
metadata (dict) --
Metadata for the workflow version.
(string) --
(string) --
nextToken (string) --
A pagination token that's included if more results are available.
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' )
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.
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.
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 )
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.
None
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', ], 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' }
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.
Deletes a workflow version. Deleting a workflow version doesn't affect any ongoing runs that are using 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.delete_workflow_version( workflowId='string', versionName='string' )
string
[REQUIRED]
The workflow's ID.
string
[REQUIRED]
The workflow version name.
None
{'storageType': 'STATIC | DYNAMIC'}Response
{'uuid': 'string'}
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 Amazon Web Services 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 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' )
string
A name for the workflow.
string
A description for the workflow.
string
The workflow engine for the workflow.
bytes
A ZIP archive for the workflow.
string
The URI of a definition for the workflow.
string
The path of the main definition file for the workflow.
dict
A parameter template for the workflow.
(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.
dict
Tags for the workflow.
(string) --
(string) --
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 computational accelerator specified to run 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.
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.
{'workflowUuid': 'string', 'workflowVersionName': 'string'}
Gets information about a workflow run.
If a workflow is shared with you, you cannot export information about the run.
Amazon Web Services HealthOmics stores a fixed number of runs that are available to the console and API. If GetRun doesn't return the requested run, you can find run logs for all runs in the CloudWatch logs. For more information about viewing the run logs, see CloudWatch logs in the in the Amazon Web Services HealthOmics User Guide.
See also: AWS API Documentation
Request Syntax
client.get_run( id='string', export=[ 'DEFINITION', ] )
string
[REQUIRED]
The run's ID.
list
The run's export format.
(string) --
dict
Response Syntax
{ 'arn': 'string', 'id': 'string', 'cacheId': 'string', 'cacheBehavior': 'CACHE_ON_FAILURE'|'CACHE_ALWAYS', 'engineVersion': 'string', 'status': 'PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'DELETED'|'CANCELLED'|'FAILED', 'workflowId': 'string', 'workflowType': 'PRIVATE'|'READY2RUN', 'runId': 'string', 'roleArn': 'string', 'name': 'string', 'runGroupId': 'string', 'priority': 123, 'definition': 'string', 'digest': 'string', 'parameters': {...}|[...]|123|123.4|'string'|True|None, 'storageCapacity': 123, 'outputUri': 'string', 'logLevel': 'OFF'|'FATAL'|'ERROR'|'ALL', 'resourceDigests': { 'string': 'string' }, 'startedBy': 'string', 'creationTime': datetime(2015, 1, 1), 'startTime': datetime(2015, 1, 1), 'stopTime': datetime(2015, 1, 1), 'statusMessage': 'string', 'tags': { 'string': 'string' }, 'accelerators': 'GPU', 'retentionMode': 'RETAIN'|'REMOVE', 'failureReason': 'string', 'logLocation': { 'engineLogStream': 'string', 'runLogStream': 'string' }, 'uuid': 'string', 'runOutputUri': 'string', 'storageType': 'STATIC'|'DYNAMIC', 'workflowOwnerId': 'string', 'workflowVersionName': 'string', 'workflowUuid': 'string' }
Response Structure
(dict) --
arn (string) --
The run's ARN.
id (string) --
The run's ID.
cacheId (string) --
The run cache associated with the run.
cacheBehavior (string) --
The run cache behavior for the run.
engineVersion (string) --
The actual Nextflow engine version that Amazon Web Services HealthOmics used for the run. The other workflow definition languages don't provide a value for this field.
status (string) --
The run's status.
workflowId (string) --
The run's workflow ID.
workflowType (string) --
The run's workflow type.
runId (string) --
The run's ID.
roleArn (string) --
The run's service role ARN.
name (string) --
The run's name.
runGroupId (string) --
The run's group ID.
priority (integer) --
The run's priority.
definition (string) --
The run's definition.
digest (string) --
The run's digest.
parameters (:ref:`document<document>`) --
The run's parameters.
storageCapacity (integer) --
The run's storage capacity in gibibytes. For dynamic storage, after the run has completed, this value is the maximum amount of storage used during the run.
outputUri (string) --
The run's output URI.
logLevel (string) --
The run's log level.
resourceDigests (dict) --
The run's resource digests.
(string) --
(string) --
startedBy (string) --
Who started the run.
creationTime (datetime) --
When the run was created.
startTime (datetime) --
When the run started.
stopTime (datetime) --
The run's stop time.
statusMessage (string) --
The run's status message.
tags (dict) --
The run's tags.
(string) --
(string) --
accelerators (string) --
The computational accelerator used to run the workflow.
retentionMode (string) --
The run's retention mode.
failureReason (string) --
The reason a run has failed.
logLocation (dict) --
The location of the run log.
engineLogStream (string) --
The log stream ARN for the engine log.
runLogStream (string) --
The log stream ARN for the run log.
uuid (string) --
The universally unique identifier for a run.
runOutputUri (string) --
The destination for workflow outputs.
storageType (string) --
The run's storage type.
workflowOwnerId (string) --
The ID of the workflow owner.
workflowVersionName (string) --
The workflow version name.
workflowUuid (string) --
The universally unique identifier (UUID) value for the workflow.
{'storageType': 'STATIC | DYNAMIC', 'uuid': 'string'}
Gets information about a workflow.
If a workflow is shared with you, you cannot export the workflow.
See also: AWS API Documentation
Request Syntax
client.get_workflow( id='string', type='PRIVATE'|'READY2RUN', export=[ 'DEFINITION', ], 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' }
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.
{'items': {'workflowVersionName': 'string'}}
Retrieves a list of runs.
Amazon Web Services HealthOmics stores a fixed number of runs that are available to the console and API. If the ListRuns response doesn't include specific runs that you expected, you can find run logs for all runs in the CloudWatch logs. For more information about viewing the run logs, see CloudWatch logs in the Amazon Web Services HealthOmics User Guide.
See also: AWS API Documentation
Request Syntax
client.list_runs( name='string', runGroupId='string', startingToken='string', maxResults=123, status='PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'DELETED'|'CANCELLED'|'FAILED' )
string
Filter the list by run name.
string
Filter the list by run group ID.
string
Specify the pagination token from a previous request to retrieve the next page of results.
integer
The maximum number of runs to return in one page of results.
string
The status of a run.
dict
Response Syntax
{ 'items': [ { 'arn': 'string', 'id': 'string', 'status': 'PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'DELETED'|'CANCELLED'|'FAILED', 'workflowId': 'string', 'name': 'string', 'priority': 123, 'storageCapacity': 123, 'creationTime': datetime(2015, 1, 1), 'startTime': datetime(2015, 1, 1), 'stopTime': datetime(2015, 1, 1), 'storageType': 'STATIC'|'DYNAMIC', 'workflowVersionName': 'string' }, ], 'nextToken': 'string' }
Response Structure
(dict) --
items (list) --
A list of runs.
(dict) --
A workflow run.
arn (string) --
The run's ARN.
id (string) --
The run's ID.
status (string) --
The run's status.
workflowId (string) --
The run's workflow ID.
name (string) --
The run's name.
priority (integer) --
The run's priority.
storageCapacity (integer) --
The run's storage capacity in gibibytes. For dynamic storage, after the run has completed, this value is the maximum amount of storage used during the run.
creationTime (datetime) --
When the run was created.
startTime (datetime) --
When the run started.
stopTime (datetime) --
When the run stopped.
storageType (string) --
The run's storage type.
workflowVersionName (string) --
The name of the workflow version.
nextToken (string) --
A pagination token that's included if more results are available.
{'workflowVersionName': 'string'}
Starts a new run or duplicates an existing run.
For a new run, specify a unique requestId, the workflowId, and a role ARN. If you're using static run storage (the default), specify the required storageCapacity.
You duplicate a run by specifing a unique requestId, the runID of the run to duplicate, and a role ARN.
For more information about the optional parameters in the StartRun request, see Starting a run in the Amazon Web Services HealthOmics User Guide.
See also: AWS API Documentation
Request Syntax
client.start_run( workflowId='string', workflowType='PRIVATE'|'READY2RUN', runId='string', roleArn='string', name='string', cacheId='string', cacheBehavior='CACHE_ON_FAILURE'|'CACHE_ALWAYS', runGroupId='string', priority=123, parameters={...}|[...]|123|123.4|'string'|True|None, storageCapacity=123, outputUri='string', logLevel='OFF'|'FATAL'|'ERROR'|'ALL', tags={ 'string': 'string' }, requestId='string', retentionMode='RETAIN'|'REMOVE', storageType='STATIC'|'DYNAMIC', workflowOwnerId='string', workflowVersionName='string' )
string
The run's workflow ID.
string
The run's workflow type.
string
The ID of a run to duplicate.
string
[REQUIRED]
A service role for the run.
string
A name for the run.
string
Identifier of the cache associated with this run. If you don't specify a cache ID, no task outputs are cached for this run.
string
The cache behavior for the run. You specify this value if you want to override the default behavior for the cache. You had set the default value when you created the cache. For more information, see Run cache behavior in the Amazon Web Services HealthOmics User Guide.
string
The run's group ID.
integer
A priority for the run.
:ref:`document<document>`
Parameters for the run.
integer
The static storage capacity (in gibibytes) for this run. This field is not required if the storage type is dynamic (the system ignores any value that you enter).
string
An output URI for the run.
string
A log level for the run.
dict
Tags for the run.
(string) --
(string) --
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 retention mode for the run. The default value is RETAIN.
Amazon Web Services HealthOmics stores a fixed number of runs that are available to the console and API. In the default mode (RETAIN), you need to remove runs manually when the number of run exceeds the maximum. If you set the retention mode to REMOVE, Amazon Web Services HealthOmics automatically removes runs (that have mode set to REMOVE) when the number of run exceeds the maximum. All run logs are available in CloudWatch logs, if you need information about a run that is no longer available to the API.
For more information about retention mode, see Specifying run retention mode in the Amazon Web Services HealthOmics User Guide.
string
The storage type for the run. By default, the run uses STATIC storage type, which allocates a fixed amount of storage. If you set the storage type to DYNAMIC, Amazon Web Services HealthOmics 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.
string
The ID of the workflow owner.
string
The name of the workflow version.
dict
Response Syntax
{ 'arn': 'string', 'id': 'string', 'status': 'PENDING'|'STARTING'|'RUNNING'|'STOPPING'|'COMPLETED'|'DELETED'|'CANCELLED'|'FAILED', 'tags': { 'string': 'string' }, 'uuid': 'string', 'runOutputUri': 'string' }
Response Structure
(dict) --
arn (string) --
Unique resource identifier for the run.
id (string) --
The run's ID.
status (string) --
The run's status.
tags (dict) --
The run's tags.
(string) --
(string) --
uuid (string) --
The universally unique identifier for a run.
runOutputUri (string) --
The destination for workflow outputs.
{'storageCapacity': 'integer', 'storageType': 'STATIC | DYNAMIC'}
Updates information about a workflow. 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 )
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.
None