Omics / Client / create_workflow

create_workflow¶

Omics.Client.create_workflow(**kwargs)¶

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.

Request Syntax

response = 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'
)

Parameters:

name (string) – Name (optional but highly recommended) for the workflow to locate relevant information in the CloudWatch logs and Amazon Web Services HealthOmics console.
description (string) – A description for the workflow.
engine (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.
definitionZip (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.
definitionUri (string) – The S3 URI of a definition for the workflow. The S3 bucket must be in the same region as the workflow.
main (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.
parameterTemplate (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.
storageCapacity (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.
tags (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) –
requestId (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.
accelerators (string) – The computational accelerator specified to run the workflow.
storageType (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.
readmeMarkdown (string) – The markdown content for the workflow’s README file. This provides documentation and usage information for users of the workflow.
parameterTemplatePath (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.
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.
definitionRepository (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) –
workflowBucketOwnerId (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.
readmeUri (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.

Return type:

dict

Returns:

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.

Exceptions

Omics.Client.exceptions.InternalServerException
Omics.Client.exceptions.ServiceQuotaExceededException
Omics.Client.exceptions.ThrottlingException
Omics.Client.exceptions.ValidationException
Omics.Client.exceptions.ConflictException
Omics.Client.exceptions.ResourceNotFoundException
Omics.Client.exceptions.AccessDeniedException
Omics.Client.exceptions.RequestTimeoutException