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Create Workflow

omics_create_workflow R Documentation

Creates a private workflow

Description

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.

Usage

omics_create_workflow(name, description, engine, definitionZip,
  definitionUri, main, parameterTemplate, storageCapacity, tags,
  requestId, accelerators, storageType, containerRegistryMap,
  containerRegistryMapUri, readmeMarkdown, parameterTemplatePath,
  readmePath, definitionRepository, workflowBucketOwnerId, readmeUri)

Arguments

name

Name (optional but highly recommended) for the workflow to locate relevant information in the CloudWatch logs and Amazon Web Services HealthOmics console.
description

A description for the workflow.
engine

The workflow engine for the workflow. By default, Amazon Web Services HealthOmics detects the engine automatically from your workflow definition. Provide a value if you have workflow definition files from more than one engine in your zip file, or to use WDL lenient.

WDL lenient is designed to handle workflows migrated from Cromwell. It supports customer Cromwell directives and some non-conformant logic. For details, see Implicit type conversion in WDL lenient in the Amazon Web Services HealthOmics User Guide.
definitionZip

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

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

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

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.
storageCapacity

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

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.
requestId

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

The computational accelerator specified to run the workflow.
storageType

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.
containerRegistryMap

(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.
containerRegistryMapUri

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

The markdown content for the workflow's README file. This provides documentation and usage information for users of the workflow.
parameterTemplatePath

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

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

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

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

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.

Value

A list with the following syntax:

list(
  arn = "string",
  id = "string",
  status = "CREATING"|"ACTIVE"|"UPDATING"|"DELETED"|"FAILED"|"INACTIVE",
  tags = list(
    "string"
  ),
  uuid = "string"
)

Request syntax

svc$create_workflow(
  name = "string",
  description = "string",
  engine = "WDL"|"NEXTFLOW"|"CWL"|"WDL_LENIENT",
  definitionZip = raw,
  definitionUri = "string",
  main = "string",
  parameterTemplate = list(
    list(
      description = "string",
      optional = TRUE|FALSE
    )
  ),
  storageCapacity = 123,
  tags = list(
    "string"
  ),
  requestId = "string",
  accelerators = "GPU",
  storageType = "STATIC"|"DYNAMIC",
  containerRegistryMap = list(
    registryMappings = list(
      list(
        upstreamRegistryUrl = "string",
        ecrRepositoryPrefix = "string",
        upstreamRepositoryPrefix = "string",
        ecrAccountId = "string"
      )
    ),
    imageMappings = list(
      list(
        sourceImage = "string",
        destinationImage = "string"
      )
    )
  ),
  containerRegistryMapUri = "string",
  readmeMarkdown = "string",
  parameterTemplatePath = "string",
  readmePath = "string",
  definitionRepository = list(
    connectionArn = "string",
    fullRepositoryId = "string",
    sourceReference = list(
      type = "BRANCH"|"TAG"|"COMMIT",
      value = "string"
    ),
    excludeFilePatterns = list(
      "string"
    )
  ),
  workflowBucketOwnerId = "string",
  readmeUri = "string"
)