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[ aws . omics ]

create-workflow-version¶

Description¶

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.

Note

Don’t include any personally identifiable information (PII) in the version name. Version names appear in the workflow version ARN.

For more information, see Workflow versioning in Amazon Web Services HealthOmics in the Amazon Web Services HealthOmics User Guide .

Synopsis¶

  create-workflow-version
--workflow-id <value>
--version-name <value>
[--definition-zip <value>]
[--definition-uri <value>]
[--accelerators <value>]
[--description <value>]
[--engine <value>]
[--main <value>]
[--parameter-template <value>]
[--request-id <value>]
[--storage-type <value>]
[--storage-capacity <value>]
[--tags <value>]
[--workflow-bucket-owner-id <value>]
[--container-registry-map <value>]
[--container-registry-map-uri <value>]
[--readme-markdown <value>]
[--parameter-template-path <value>]
[--readme-path <value>]
[--definition-repository <value>]
[--readme-uri <value>]
[--cli-input-json <value>]
[--generate-cli-skeleton <value>]
[--debug]
[--endpoint-url <value>]
[--no-verify-ssl]
[--no-paginate]
[--output <value>]
[--query <value>]
[--profile <value>]
[--region <value>]
[--version <value>]
[--color <value>]
[--no-sign-request]
[--ca-bundle <value>]
[--cli-read-timeout <value>]
[--cli-connect-timeout <value>]

Options¶

--workflow-id (string)

The ID of the workflow where you are creating the new version. The workflowId is not the UUID.

--version-name (string)

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.

--definition-zip (blob)

A ZIP archive containing the main workflow definition file and dependencies that it imports for this workflow version. 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 .

--definition-uri (string)

The S3 URI of a definition for this workflow version. The S3 bucket must be in the same region as this workflow version.

--accelerators (string)

The computational accelerator for this workflow version.

Possible values:

GPU

--description (string)

A description for this workflow version.

--engine (string)

The workflow engine for this workflow version. 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.

Possible values:

WDL

NEXTFLOW

CWL

--main (string)

The path of the main definition file for this workflow version. 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 .

--parameter-template (map)

A parameter template for this workflow version. 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 .

key -> (string)

value -> (structure)

A workflow parameter.

description -> (string)

The parameter’s description.

optional -> (boolean)

Whether the parameter is optional.

Shorthand Syntax:

KeyName1=description=string,optional=boolean,KeyName2=description=string,optional=boolean

JSON Syntax:

{"string": {
      "description": "string",
      "optional": true|false
    }
  ...}

--request-id (string)

An idempotency token to ensure that duplicate workflows are not created when Amazon Web Services HealthOmics submits retry requests.

--storage-type (string)

The default storage type for runs that use this workflow version. 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 .

Possible values:

STATIC

DYNAMIC

--storage-capacity (integer)

The default static storage capacity (in gibibytes) for runs that use this workflow version. The storageCapacity can be overwritten at run time. The storage capacity is not required for runs with a DYNAMIC storage type.

--tags (map)

Tags for this workflow version. 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 .

key -> (string)

value -> (string)

Shorthand Syntax:

KeyName1=string,KeyName2=string

JSON Syntax:

{"string": "string"
  ...}

--workflow-bucket-owner-id (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.

--container-registry-map (structure)

(Optional) 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 .

registryMappings -> (list)

Mapping that provides the ECR repository path where upstream container images are pulled and synchronized.

(structure)

If you are using the ECR pull through cache feature, the registry mapping maps between the ECR repository and the upstream registry where container images are pulled and synchronized.

upstreamRegistryUrl -> (string)

The URI of the upstream registry.

ecrRepositoryPrefix -> (string)

The repository prefix to use in the ECR private repository.

upstreamRepositoryPrefix -> (string)

The repository prefix of the corresponding repository in the upstream registry.

ecrAccountId -> (string)

Account ID of the account that owns the upstream container image.

imageMappings -> (list)

Image mappings specify path mappings between the ECR private repository and their corresponding external repositories.

(structure)

Specifies image mappings that workflow tasks can use. For example, you can replace all the task references of a public image to use an equivalent image in your private ECR repository. You can use image mappings with upstream registries that don’t support pull through cache. You need to manually synchronize the upstream registry with your private repository.

sourceImage -> (string)

Specifies the URI of the source image in the upstream registry.

destinationImage -> (string)

Specifies the URI of the corresponding image in the private ECR registry.

Shorthand Syntax:

registryMappings=[{upstreamRegistryUrl=string,ecrRepositoryPrefix=string,upstreamRepositoryPrefix=string,ecrAccountId=string},{upstreamRegistryUrl=string,ecrRepositoryPrefix=string,upstreamRepositoryPrefix=string,ecrAccountId=string}],imageMappings=[{sourceImage=string,destinationImage=string},{sourceImage=string,destinationImage=string}]

JSON Syntax:

{
  "registryMappings": [
    {
      "upstreamRegistryUrl": "string",
      "ecrRepositoryPrefix": "string",
      "upstreamRepositoryPrefix": "string",
      "ecrAccountId": "string"
    }
    ...
  ],
  "imageMappings": [
    {
      "sourceImage": "string",
      "destinationImage": "string"
    }
    ...
  ]
}

--container-registry-map-uri (string)

(Optional) URI of the S3 location for the registry mapping file.

--readme-markdown (string)

The markdown content for the workflow version’s README file. This provides documentation and usage information for users of this specific workflow version.

--parameter-template-path (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.

--readme-path (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.

--definition-repository (structure)

The repository information for the workflow version definition. This allows you to source your workflow version definition directly from a code repository.

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 -> (structure)

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.

excludeFilePatterns -> (list)

A list of file patterns to exclude when retrieving the workflow definition from the repository.

(string)

Shorthand Syntax:

connectionArn=string,fullRepositoryId=string,sourceReference={type=string,value=string},excludeFilePatterns=string,string

JSON Syntax:

{
  "connectionArn": "string",
  "fullRepositoryId": "string",
  "sourceReference": {
    "type": "BRANCH"|"TAG"|"COMMIT",
    "value": "string"
  },
  "excludeFilePatterns": ["string", ...]
}

--readme-uri (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.

--cli-input-json (string) Performs service operation based on the JSON string provided. The JSON string follows the format provided by --generate-cli-skeleton. If other arguments are provided on the command line, the CLI values will override the JSON-provided values. It is not possible to pass arbitrary binary values using a JSON-provided value as the string will be taken literally.

--generate-cli-skeleton (string) Prints a JSON skeleton to standard output without sending an API request. If provided with no value or the value input, prints a sample input JSON that can be used as an argument for --cli-input-json. If provided with the value output, it validates the command inputs and returns a sample output JSON for that command.

Global Options¶

--debug (boolean)

Turn on debug logging.

--endpoint-url (string)

Override command’s default URL with the given URL.

--no-verify-ssl (boolean)

By default, the AWS CLI uses SSL when communicating with AWS services. For each SSL connection, the AWS CLI will verify SSL certificates. This option overrides the default behavior of verifying SSL certificates.

--no-paginate (boolean)

Disable automatic pagination. If automatic pagination is disabled, the AWS CLI will only make one call, for the first page of results.

--output (string)

The formatting style for command output.

json
text
table

--query (string)

A JMESPath query to use in filtering the response data.

--profile (string)

Use a specific profile from your credential file.

--region (string)

The region to use. Overrides config/env settings.

--version (string)

Display the version of this tool.

--color (string)

Turn on/off color output.

on
off
auto

--no-sign-request (boolean)

Do not sign requests. Credentials will not be loaded if this argument is provided.

--ca-bundle (string)

The CA certificate bundle to use when verifying SSL certificates. Overrides config/env settings.

--cli-read-timeout (int)

The maximum socket read time in seconds. If the value is set to 0, the socket read will be blocking and not timeout. The default value is 60 seconds.

--cli-connect-timeout (int)

The maximum socket connect time in seconds. If the value is set to 0, the socket connect will be blocking and not timeout. The default value is 60 seconds.

Output¶

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 -> (map)

The workflow version’s tags.

key -> (string)

value -> (string)

uuid -> (string)

The universally unique identifier (UUID) value for this workflow version.

Table of Contents

Feedback

User Guide

Note:

create-workflow-version¶

Description¶

Note

Synopsis¶

Options¶

Global Options¶

Output¶