Amazon HealthOmics Healthomics Runbatch API

openapi: 3.2.0
info:
  title: Amazon Omics Runbatch API
  version: '2022-11-28'
  description: Generated from AWS's published Smithy model for Amazon Omics. 6 operation(s).
  contact:
    name: Amazon Web Services
    url: https://aws.amazon.com/contact-us/
  license:
    name: Apache 2.0
    identifier: Apache-2.0
    url: https://github.com/aws/api-models-aws/blob/main/LICENSE
servers:
- url: https://omics.{region}.amazonaws.com
  variables:
    region:
      default: us-east-1
security:
- sigv4: []
tags:
- name: Runbatch
paths:
  /runBatch/cancel:
    post:
      operationId: CancelRunBatch
      summary: Cancel Run Batch
      description: Cancels all runs within a specified batch. This operation prevents not-yet-submitted runs from starting and submits CancelRun requests for runs that have already started. Cancel is only allowed on batches in PENDING, SUBMITTING, or INPROGRESS state. Cancel operations are non-atomic and may be partially successful. Use GetBatch to review successfulCancelSubmissionCount and failedCancelSubmissionCount in the submissionSummary. Only one cancel or delete operation per batch is allowed at a time.
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/CancelRunBatchResponse'
        '403':
          description: AccessDeniedException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AccessDeniedException'
        '409':
          description: ConflictException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ConflictException'
        '500':
          description: InternalServerException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/InternalServerException'
        '408':
          description: RequestTimeoutException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/RequestTimeoutException'
        '404':
          description: ResourceNotFoundException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ResourceNotFoundException'
        '402':
          description: ServiceQuotaExceededException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ServiceQuotaExceededException'
        '429':
          description: ThrottlingException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ThrottlingException'
        '400':
          description: ValidationException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ValidationException'
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/CancelRunBatchRequest'
      tags:
      - Runbatch
  /runBatch/delete:
    post:
      operationId: DeleteRunBatch
      summary: Delete Run Batch
      description: Deletes the individual workflow runs within a batch. This operation is separate from DeleteBatch, which removes the batch metadata. Delete is only allowed on batches in PROCESSED or CANCELLED state. Delete operations are non-atomic and may be partially successful. Use GetBatch to review successfulDeleteSubmissionCount and failedDeleteSubmissionCount in the submissionSummary. Only one cancel or delete operation per batch is allowed at a time.
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/DeleteRunBatchResponse'
        '403':
          description: AccessDeniedException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AccessDeniedException'
        '409':
          description: ConflictException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ConflictException'
        '500':
          description: InternalServerException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/InternalServerException'
        '408':
          description: RequestTimeoutException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/RequestTimeoutException'
        '404':
          description: ResourceNotFoundException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ResourceNotFoundException'
        '402':
          description: ServiceQuotaExceededException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ServiceQuotaExceededException'
        '429':
          description: ThrottlingException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ThrottlingException'
        '400':
          description: ValidationException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ValidationException'
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/DeleteRunBatchRequest'
      tags:
      - Runbatch
  /runBatch:
    post:
      operationId: StartRunBatch
      summary: Start Run Batch
      description: Starts a batch of workflow runs. You can group up to 100,000 runs into a single batch that share a common configuration defined in defaultRunSetting. Per-run overrides can be provided either inline via inlineSettings (up to 100 runs) or via a JSON file stored in Amazon S3 via s3UriSettings (up to 100,000 runs). StartRunBatch validates common fields synchronously and returns immediately with a batch ID and status CREATING. The batch transitions to PENDING once initial setup completes. Runs are then submitted gradually and asynchronously at a rate governed by your StartRun throughput quota.
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/StartRunBatchResponse'
        '403':
          description: AccessDeniedException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AccessDeniedException'
        '409':
          description: ConflictException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ConflictException'
        '500':
          description: InternalServerException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/InternalServerException'
        '408':
          description: RequestTimeoutException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/RequestTimeoutException'
        '404':
          description: ResourceNotFoundException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ResourceNotFoundException'
        '402':
          description: ServiceQuotaExceededException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ServiceQuotaExceededException'
        '429':
          description: ThrottlingException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ThrottlingException'
        '400':
          description: ValidationException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ValidationException'
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/StartRunBatchRequest'
      tags:
      - Runbatch
    get:
      operationId: ListBatch
      summary: List Batch
      description: Returns a list of run batches in your account, with optional filtering by status, name, or run group. Results are paginated. Only one filter per call is supported.
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ListBatchResponse'
        '403':
          description: AccessDeniedException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AccessDeniedException'
        '500':
          description: InternalServerException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/InternalServerException'
        '408':
          description: RequestTimeoutException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/RequestTimeoutException'
        '429':
          description: ThrottlingException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ThrottlingException'
        '400':
          description: ValidationException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ValidationException'
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/ListBatchRequest'
      tags:
      - Runbatch
  /runBatch/{batchId}:
    get:
      operationId: GetBatch
      summary: Get Batch
      description: Retrieves details and current status for a specific run batch, including submission progress and run execution counts.
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/GetBatchResponse'
        '403':
          description: AccessDeniedException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AccessDeniedException'
        '500':
          description: InternalServerException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/InternalServerException'
        '408':
          description: RequestTimeoutException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/RequestTimeoutException'
        '404':
          description: ResourceNotFoundException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ResourceNotFoundException'
        '429':
          description: ThrottlingException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ThrottlingException'
        '400':
          description: ValidationException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ValidationException'
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/GetBatchRequest'
      tags:
      - Runbatch
    delete:
      operationId: DeleteBatch
      summary: Delete Batch
      description: 'Deletes a run batch resource and its associated metadata. This operation does not delete the individual workflow runs. To delete the runs, call DeleteRunBatch before calling DeleteBatch. DeleteBatch requires the batch to be in a terminal state: PROCESSED, FAILED, CANCELLED, RUNS_DELETE_FAILED, or RUNS_DELETED. After DeleteBatch completes, the batch metadata is no longer accessible. You cannot call GetBatch, ListRunsInBatch, DeleteRunBatch, or CancelRunBatch on a deleted batch.'
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                type: string
        '403':
          description: AccessDeniedException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AccessDeniedException'
        '409':
          description: ConflictException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ConflictException'
        '500':
          description: InternalServerException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/InternalServerException'
        '408':
          description: RequestTimeoutException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/RequestTimeoutException'
        '404':
          description: ResourceNotFoundException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ResourceNotFoundException'
        '402':
          description: ServiceQuotaExceededException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ServiceQuotaExceededException'
        '429':
          description: ThrottlingException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ThrottlingException'
        '400':
          description: ValidationException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ValidationException'
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/DeleteBatchRequest'
      tags:
      - Runbatch
components:
  schemas:
    GetBatchResponse:
      type: object
      properties:
        id:
          type: string
          description: The identifier portion of the run batch ARN.
        arn:
          type: string
          description: The unique ARN of the run batch.
        uuid:
          type: string
          description: The universally unique identifier (UUID) for the run batch.
        name:
          type: string
          description: The optional user-friendly name of the batch.
        status:
          type: string
          description: 'The current status of the run batch. Possible values: CREATING (initial setup), PENDING (ready to submit runs), SUBMITTING (submitting runs), INPROGRESS (runs executing), STOPPING (cancellation in progress), PROCESSED (all runs completed), CANCELLED (batch cancelled), FAILED (batch failed), RUNS_DELETING (deleting runs), RUNS_DELETE_FAILED (run deletion failed for some or all runs), RUNS_DELETED (runs deleted).'
        tags:
          type: object
          additionalProperties:
            type: string
          description: Amazon Web Services tags associated with the run batch.
        totalRuns:
          type: integer
          description: The total number of runs in the batch.
        defaultRunSetting:
          $ref: '#/components/schemas/DefaultRunSetting'
        submissionSummary:
          $ref: '#/components/schemas/SubmissionSummary'
        runSummary:
          $ref: '#/components/schemas/RunSummary'
        creationTime:
          type: string
          format: date-time
          description: The timestamp when the batch was created.
        submittedTime:
          type: string
          format: date-time
          description: The timestamp when all run submissions completed.
        processedTime:
          type: string
          format: date-time
          description: The timestamp when all run executions completed.
        failedTime:
          type: string
          format: date-time
          description: The timestamp when the batch transitioned to a FAILED status.
        failureReason:
          type: string
          description: A description of the batch failure. Present only when status is FAILED.
    CancelRunBatchRequest:
      type: object
      properties:
        batchId:
          type: string
          description: The identifier portion of the run batch ARN.
      required:
      - batchId
    RequestTimeoutException:
      type: object
      properties:
        message:
          type: string
      required:
      - message
    ListBatchRequest:
      type: object
      properties:
        maxItems:
          type: integer
          description: The maximum number of batches to return. If not specified, defaults to 100.
        startingToken:
          type: string
          description: A pagination token returned from a prior ListBatch call.
        status:
          type: string
          description: Filter batches by status.
        name:
          type: string
          description: Filter batches by name.
        runGroupId:
          type: string
          description: Filter batches by run group ID.
    RunSummary:
      type: object
      properties:
        pendingRunCount:
          type: integer
          description: The number of pending runs.
        startingRunCount:
          type: integer
          description: The number of starting runs.
        runningRunCount:
          type: integer
          description: The number of running runs.
        stoppingRunCount:
          type: integer
          description: The number of stopping runs.
        completedRunCount:
          type: integer
          description: The number of completed runs.
        deletedRunCount:
          type: integer
          description: The number of deleted runs.
        failedRunCount:
          type: integer
          description: The number of failed runs.
        cancelledRunCount:
          type: integer
          description: The number of cancelled runs.
    DeleteRunBatchResponse:
      type: object
      properties: {}
    StartRunBatchRequest:
      type: object
      properties:
        batchName:
          type: string
          description: An optional user-friendly name for the run batch.
        requestId:
          type: string
          description: A client token used to deduplicate retry requests and prevent duplicate batches from being created.
        tags:
          type: object
          additionalProperties:
            type: string
          description: Amazon Web Services tags to associate with the batch resource. These tags are not inherited by individual runs. To tag individual runs, use defaultRunSetting.runTags.
        defaultRunSetting:
          $ref: '#/components/schemas/DefaultRunSetting'
        batchRunSettings:
          $ref: '#/components/schemas/BatchRunSettings'
      required:
      - requestId
      - defaultRunSetting
      - batchRunSettings
    AccessDeniedException:
      type: object
      properties:
        message:
          type: string
      required:
      - message
    DeleteBatchRequest:
      type: object
      properties:
        batchId:
          type: string
          description: The identifier portion of the run batch ARN.
      required:
      - batchId
    BatchRunSettings:
      type: object
      properties:
        inlineSettings:
          type: array
          items:
            $ref: '#/components/schemas/InlineSetting'
          description: A list of per-run configurations provided inline in the request. Each entry must include a unique runSettingId. Supports up to 100 entries. For batches with more than 100 runs, use s3UriSettings.
        s3UriSettings:
          type: string
          description: An Amazon S3 URI pointing to a JSON file containing per-run configurations. The file must be a JSON array in the same format as inlineSettings. Supports up to 100,000 run configurations. The maximum file size is 6 GB. The IAM service role in roleArn must have read access to this S3 object. HealthOmics validates access to the file during the synchronous API call and records the file's ETag. If the file is modified after submission, the batch fails.
      description: Exactly one member is set.
    SubmissionSummary:
      type: object
      properties:
        successfulStartSubmissionCount:
          type: integer
          description: The number of successful start submissions.
        failedStartSubmissionCount:
          type: integer
          description: The number of failed start submissions.
        pendingStartSubmissionCount:
          type: integer
          description: The number of pending start submissions.
        successfulCancelSubmissionCount:
          type: integer
          description: The number of successful cancel submissions.
        failedCancelSubmissionCount:
          type: integer
          description: The number of failed cancel submissions.
        successfulDeleteSubmissionCount:
          type: integer
          description: The number of successful delete submissions.
        failedDeleteSubmissionCount:
          type: integer
          description: The number of failed delete submissions.
    DeleteRunBatchRequest:
      type: object
      properties:
        batchId:
          type: string
          description: The identifier portion of the run batch ARN.
      required:
      - batchId
    InlineSetting:
      type: object
      properties:
        runSettingId:
          type: string
          description: A customer-provided unique identifier for this run configuration within the batch. After submission, use ListRunsInBatch to map each runSettingId to the HealthOmics-generated runId.
        name:
          type: string
          description: An optional user-friendly name for this run.
        outputUri:
          type: string
          description: Override the destination S3 URI for this run's outputs.
        priority:
          type: integer
          description: Override the priority for this run.
        parameters:
          type: object
          description: Per-run workflow parameters. Merged with defaultRunSetting.parameters; values in this object take precedence when keys overlap.
        outputBucketOwnerId:
          type: string
          description: The expected Amazon Web Services account ID of the owner of the output S3 bucket for this run.
        runTags:
          type: object
          additionalProperties:
            type: string
          description: Per-run Amazon Web Services tags. Merged with defaultRunSetting.runTags; values in this object take precedence when keys overlap.
        engineSettings:
          type: object
          description: Per-run engine-specific settings. Use this field to specify configuration options that are specific to the workflow engine (for example, Nextflow profiles). Overrides defaultRunSetting.engineSettings for this run.
      required:
      - runSettingId
    DefaultRunSetting:
      type: object
      properties:
        workflowId:
          type: string
          description: The identifier of the workflow to run.
        workflowType:
          type: string
          description: The type of the originating workflow. Batch runs are not supported with READY2RUN workflows.
        roleArn:
          type: string
          description: The IAM role ARN that grants HealthOmics permissions to access required Amazon Web Services resources such as Amazon S3 and CloudWatch. The role must have the same permissions required for individual StartRun calls.
        name:
          type: string
          description: An optional user-friendly name applied to each workflow run. Can be overridden per run.
        cacheId:
          type: string
          description: The identifier of the run cache to associate with the runs.
        cacheBehavior:
          type: string
          description: The cache behavior for the runs. Requires cacheId to be set.
        runGroupId:
          type: string
          description: The ID of the run group to contain all workflow runs in the batch.
        priority:
          type: integer
          description: An integer priority for the workflow runs. Higher values correspond to higher priority. A value of 0 corresponds to the lowest priority. Can be overridden per run.
        parameters:
          type: object
          description: Workflow parameter names and values shared across all runs. Merged with per-run parameters; run-specific values take precedence when keys overlap. Can be overridden per run.
        storageCapacity:
          type: integer
          description: The filesystem size in gibibytes (GiB) provisioned for each workflow run and shared by all tasks in that run. Defaults to 1200 GiB if not specified.
        outputUri:
          type: string
          description: The destination S3 URI for workflow outputs. Must begin with s3://. The roleArn must grant write permissions to this bucket. Can be overridden per run.
        logLevel:
          type: string
          description: The verbosity level for CloudWatch Logs emitted during each run.
        runTags:
          type: object
          additionalProperties:
            type: string
          description: Amazon Web Services tags to associate with each workflow run. Merged with per-run runTags; run-specific values take precedence when keys overlap.
        retentionMode:
          type: string
          description: The retention behavior for runs after completion.
        storageType:
          type: string
          description: The storage type for the workflow runs.
        workflowOwnerId:
          type: string
          description: The Amazon Web Services account ID of the workflow owner, used for cross-account workflow sharing.
        outputBucketOwnerId:
          type: string
          description: The expected Amazon Web Services account ID of the owner of the output S3 bucket. Can be overridden per run.
        workflowVersionName:
          type: string
          description: The version name of the specified workflow.
        networkingMode:
          type: string
          description: Optional configuration for run networking behavior. If not specified, this will default to RESTRICTED.
        configurationName:
          type: string
          description: Optional configuration name to use for the workflow run.
        sessionPolicy:
          type: string
          description: Optional inline policy json for scoping down permissions via a session policy on the IAM role provided in the roleArn parameter.
        engineSettings:
          type: object
          description: Engine-specific settings for the workflow run. Use this field to specify configuration options that are specific to the workflow engine (for example, Nextflow profiles).
        scratchStorageMode:
          type: string
          description: Optional configuration for enabling scratch ephemeral storage mounted at /tmp. If not specified, this will default to SHARED. This configuration is applicable only for CPU tasks. For tasks using GPUs, scratch storage is always LOCAL.
      required:
      - workflowId
      - roleArn
    BatchListItem:
      type: object
      properties:
        id:
          type: string
          description: The batch identifier.
        name:
          type: string
          description: The batch name.
        status:
          type: string
          description: The current batch status.
        createdAt:
          type: string
          format: date-time
          description: The timestamp when the batch was created.
        totalRuns:
          type: integer
          description: The total number of runs in the batch.
        workflowId:
          type: string
          description: The identifier of the workflow used for the batch.
    ServiceQuotaExceededException:
      type: object
      properties:
        message:
          type: string
      required:
      - message
    ConflictException:
      type: object
      properties:
        message:
          type: string
      required:
      - message
    ListBatchResponse:
      type: object
      properties:
        items:
          type: array
          items:
            $ref: '#/components/schemas/BatchListItem'
          description: A list of batch summary objects. See BatchListItem.
        nextToken:
          type: string
          description: A pagination token to retrieve the next page of results. Absent when no further results are available.
    StartRunBatchResponse:
      type: object
      properties:
        id:
          type: string
          description: The identifier portion of the run batch ARN.
        arn:
          type: string
          description: The unique ARN of the run batch.
        status:
          type: string
          description: The initial status of the run batch. Returns CREATING while the batch is being initialized.
        uuid:
          type: string
          description: The universally unique identifier (UUID) for the run batch.
        tags:
          type: object
          additionalProperties:
            type: string
          description: Amazon Web Services tags associated with the run batch.
    GetBatchRequest:
      type: object
      properties:
        batchId:
          type: string
          description: The identifier portion of the run batch ARN.
      required:
      - batchId
    CancelRunBatchResponse:
      type: object
      properties: {}
    ValidationException:
      type: object
      properties:
        message:
          type: string
      required:
      - message
    ResourceNotFoundException:
      type: object
      properties:
        message:
          type: string
      required:
      - message
    InternalServerException:
      type: object
      properties:
        message:
          type: string
      required:
      - message
    ThrottlingException:
      type: object
      properties:
        message:
          type: string
      required:
      - message
  securitySchemes:
    sigv4:
      type: apiKey
      in: header
      name: Authorization
      description: AWS Signature Version 4. The Authorization header carries an AWS4-HMAC-SHA256 signature over the canonical request, with X-Amz-Date (and X-Amz-Security-Token for temporary credentials). Not a bearer token.
      x-aws-sigv4:
        signingName: omics
x-provenance:
  method: harvested
  publisher: Amazon Web Services
  source: https://raw.githubusercontent.com/aws/api-models-aws/582e55931c45b944739742a2c1620b6026dd2d13/models/omics/service/2022-11-28/omics-2022-11-28.json
  note: converted by smithy-to-openapi.py from AWS's Smithy model (roadmap#1001)