Start Run

omics_start_run

R Documentation

Starts a new run and returns details about the run, or duplicates an existing run¶

Description¶

Starts a new run and returns details about the run, or duplicates an existing run. A run is a single invocation of a workflow. If you provide request IDs, Amazon Web Services HealthOmics identifies duplicate requests and starts the run only once. Monitor the progress of the run by calling the get_run API operation.

To start a new run, the following inputs are required:

A service role ARN (roleArn).
The run's workflow ID (workflowId, not the uuid or runId).
An Amazon S3 location (outputUri) where the run outputs will be saved.
All required workflow parameters (parameter), which can include optional parameters from the parameter template. The run cannot include any parameters that are not defined in the parameter template. To see all possible parameters, use the get_run API operation.
For runs with a STATIC (default) storage type, specify the required storage capacity (in gibibytes). A storage capacity value is not required for runs that use DYNAMIC storage.

start_run can also duplicate an existing run using the run's default values. You can modify these default values and/or add other optional inputs. To duplicate a run, the following inputs are required:

A service role ARN (roleArn).
The ID of the run to duplicate (runId).
An Amazon S3 location where the run outputs will be saved (outputUri).

To learn more about the optional parameters for start_run, see Starting a run in the Amazon Web Services HealthOmics User Guide.

Use the retentionMode input to control how long the metadata for each run is stored in CloudWatch. There are two retention modes:

Specify REMOVE to automatically remove the oldest runs when you reach the maximum service retention limit for runs. It is recommended that you use the REMOVE mode to initiate major run requests so that your runs do not fail when you reach the limit.
The retentionMode is set to the RETAIN mode by default, which allows you to manually remove runs after reaching the maximum service retention limit. Under this setting, you cannot create additional runs until you remove the excess runs.

To learn more about the retention modes, see Run retention mode in the Amazon Web Services HealthOmics User Guide.

You can use Amazon Q CLI to analyze run logs and make performance optimization recommendations. To get started, see the Amazon Web Services HealthOmics MCP server on GitHub.

Usage¶

omics_start_run(workflowId, workflowType, runId, roleArn, name, cacheId,
  cacheBehavior, runGroupId, priority, parameters, storageCapacity,
  outputUri, logLevel, tags, requestId, retentionMode, storageType,
  workflowOwnerId, workflowVersionName, networkingMode, configurationName)

Arguments¶

workflowId

The run's workflow ID. The workflowId is not the UUID.

workflowType

The run's workflow type. The workflowType must be specified if you are running a READY2RUN workflow. If you are running a PRIVATE workflow (default), you do not need to include the workflow type.

runId

The ID of a run to duplicate.

roleArn

[required] A service role for the run. The roleArn requires access to Amazon Web Services HealthOmics, S3, Cloudwatch logs, and EC2. An example roleArn is ⁠arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ⁠. In this example, the AWS account ID is 123456789012 and the role name is omics-service-role-serviceRole-W8O1XMPL7QZ.

name

A name for the run. This is recommended to view and organize runs in the Amazon Web Services HealthOmics console and CloudWatch logs.

cacheId

Identifier of the cache associated with this run. If you don't specify a cache ID, no task outputs are cached for this run.

cacheBehavior

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.

runGroupId

The run's group ID. Use a run group to cap the compute resources (and number of concurrent runs) for the runs that you add to the run group.

priority

Use the run priority (highest: 1) to establish the order of runs in a run group when you start a run. If multiple runs share the same priority, the run that was initiated first will have the higher priority. Runs that do not belong to a run group can be assigned a priority. The priorities of these runs are ranked among other runs that are not in a run group. For more information, see Run priority in the Amazon Web Services HealthOmics User Guide.

parameters

Parameters for the run. The run needs all required parameters and can include optional parameters. The run cannot include any parameters that are not defined in the parameter template. To retrieve parameters from the run, use the GetRun API operation.

storageCapacity

The STATIC storage capacity (in gibibytes, GiB) for this run. The default run storage capacity is 1200 GiB. If your requested storage capacity is unavailable, the system rounds up the value to the nearest 1200 GiB multiple. If the requested storage capacity is still unavailable, the system rounds up the value to the nearest 2400 GiB multiple. This field is not required if the storage type is DYNAMIC (the system ignores any value that you enter).

outputUri

[required] An output S3 URI for the run. The S3 bucket must be in the same region as the workflow. The role ARN must have permission to write to this S3 bucket.

logLevel

A log level for the run.

tags

Tags for the run. You can add up to 50 tags per run. For more information, see Adding a tag in the Amazon Web Services HealthOmics User Guide.

requestId

[required] An idempotency token used to dedupe retry requests so that duplicate runs are not created.

retentionMode

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.

storageType

The storage type for the run. If you set the storage type to DYNAMIC, Amazon Web Services HealthOmics dynamically scales the storage up or down, based on file system utilization. By default, the run uses STATIC storage type, which allocates a fixed amount of storage. For more information about DYNAMIC and STATIC storage, see Run storage types in the Amazon Web Services HealthOmics User Guide.

workflowOwnerId

The 12-digit account ID of the workflow owner that is used for running a shared workflow. The workflow owner ID can be retrieved using the get_share API operation. If you are the workflow owner, you do not need to include this ID.

workflowVersionName

The name of the workflow version. Use workflow versions to track and organize changes to the workflow. If your workflow has multiple versions, the run uses the default version unless you specify a version name. To learn more, see Workflow versioning in the Amazon Web Services HealthOmics User Guide.

networkingMode

Optional configuration for run networking behavior. If not specified, this will default to RESTRICTED.

configurationName

Optional configuration name to use for the workflow run.

Value¶

A list with the following syntax:

list(
  arn = "string",
  id = "string",
  status = "PENDING"|"STARTING"|"RUNNING"|"STOPPING"|"COMPLETED"|"DELETED"|"CANCELLED"|"FAILED",
  tags = list(
    "string"
  ),
  uuid = "string",
  runOutputUri = "string",
  configuration = list(
    name = "string",
    arn = "string",
    uuid = "string"
  ),
  networkingMode = "string"
)

Request syntax¶

svc$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 = list(),
  storageCapacity = 123,
  outputUri = "string",
  logLevel = "OFF"|"FATAL"|"ERROR"|"ALL",
  tags = list(
    "string"
  ),
  requestId = "string",
  retentionMode = "RETAIN"|"REMOVE",
  storageType = "STATIC"|"DYNAMIC",
  workflowOwnerId = "string",
  workflowVersionName = "string",
  networkingMode = "RESTRICTED"|"VPC",
  configurationName = "string"
)