Stops a multipart upload.

Accept a resource share request.

Deletes one or more read sets.

Cancels an annotation import job.

Cancels a run using its ID and returns a response with no body if the operation is successful.

To confirm that the run has been cancelled, use the ListRuns API operation to check that it is no longer listed.

Cancels a variant import job.

Concludes a multipart upload once you have uploaded all the components.

Creates an annotation store.

Creates a new version of an annotation store.

Begins a multipart read set upload.

Creates a reference store.

Creates a run cache to store and reference task outputs from completed private runs.

Specify an Amazon S3 location where Amazon Web Services HealthOmics saves the cached data. This data must be immediately accessible and not in an archived state. You can save intermediate task files to a run cache if they are declared as task outputs in the workflow definition file.

For more information, see Call caching and Creating a run cache in the Amazon Web Services HealthOmics User Guide.

Creates a run group to limit the compute resources for the runs that are added to the group.

Returns an ARN, ID, and tags for the run group.

Creates a sequence store.

Creates a cross-account shared resource.

The resource owner makes an offer to share the resource with the principal subscriber (an AWS user with a different account than the resource owner).

The following resources support cross-account sharing:

• HealthOmics variant stores

• HealthOmics annotation stores

• Private workflows

Creates a variant store.

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.

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.

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.

Deletes an annotation store.

Deletes one or multiple versions of an annotation store.

Deletes a genome reference.

Deletes a genome reference store.

Deletes a run and returns a response with no body if the operation is successful.

You can only delete a run that has reached a COMPLETED, FAILED, or CANCELLED stage. A completed run has delivered an output, or was cancelled and resulted in no output. When you delete a run, only the metadata associated with the run is deleted. The run outputs remain in Amazon S3 and logs remain in CloudWatch.

To verify that the workflow is deleted:

• Use ListRuns to confirm the workflow no longer appears in the list.

• Use GetRun to verify the workflow cannot be found.

Deletes a run cache and returns a response with no body if the operation is successful.

This action removes the cache metadata stored in the service account, but does not delete the data in Amazon S3. You can access the cache data in Amazon S3, for inspection or to troubleshoot issues. You can remove old cache data using standard S3 Delete operations.

For more information, see Deleting a run cache in the Amazon Web Services HealthOmics User Guide.

Deletes a run group and returns a response with no body if the operation is successful.

To verify that the run group is deleted:

• Use ListRunGroups to confirm the workflow no longer appears in the list.

• Use GetRunGroup to verify the workflow cannot be found.

Deletes an access policy for the specified store.

Deletes a sequence store.

Deletes a resource share.

If you are the resource owner, the subscriber will no longer have access to the shared resource. If you are the subscriber, this operation deletes your access to the share.

Deletes a variant store.

Deletes a workflow by specifying its ID.

No response is returned if the deletion is successful.

To verify that the workflow is deleted:

• Use ListWorkflows to confirm the workflow no longer appears in the list.

• Use GetWorkflow to verify the workflow cannot be found.

Deletes a workflow version.

Deleting a workflow version doesn't affect any ongoing runs that are using the workflow version.

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

Gets information about an annotation import job.

Gets information about an annotation store.

Retrieves the metadata for an annotation store version.

Gets a file from a read set.

Gets information about a read set activation job.

Gets information about a read set export job.

Gets information about a read set import job.

Gets details about a read set.

Gets a reference file.

Gets information about a reference import job.

Gets information about a genome reference's metadata.

Gets information about a reference store.

Gets detailed information about a specific run using its ID.

Amazon Web Services HealthOmics stores a configurable number of runs, as determined by service limits, that are available to the console and API. If GetRun does not return the requested run, you can find all run logs in the CloudWatch logs. For more information about viewing the run logs, see CloudWatch logs in the Amazon Web Services HealthOmics User Guide.

Retrieves detailed information about the specified run cache using its ID.

For more information, see Call caching for Amazon Web Services HealthOmics runs in the Amazon Web Services HealthOmics User Guide.

Gets information about a run group and returns its metadata.

Gets detailed information about a run task using its ID.

Retrieves details about an access policy on a given store.

Gets information about a sequence store.

Retrieves the metadata for the specified resource share.

Gets information about a variant import job.

Gets information about a variant store.

Gets all information about a workflow using its ID.

If a workflow is shared with you, you cannot export the workflow.

For more information about your workflow status, see Verify the workflow status in the Amazon Web Services HealthOmics User Guide.

Gets information about a workflow version.

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

Retrieves a list of annotation import jobs.

Lists the versions of an annotation store.

Retrieves a list of annotation stores.

Lists multipart read set uploads and for in progress uploads.

Once the upload is completed, a read set is created and the upload will no longer be returned in the response.

Retrieves a list of read set activation jobs.

Retrieves a list of read set export jobs.

Retrieves a list of read set import jobs.

This operation will list all parts in a requested multipart upload for a sequence store.

Retrieves a list of read sets.

Retrieves a list of reference import jobs.

Retrieves a list of reference stores.

Retrieves a list of references.

Retrieves a list of your run caches and the metadata for each cache.

Retrieves a list of all run groups and returns the metadata for each run group.

Returns a list of tasks and status information within their specified run.

Use this operation to monitor runs and to identify which specific tasks have failed.

Retrieves a list of runs and returns each run's metadata and status.

Amazon Web Services HealthOmics stores a configurable number of runs, as determined by service limits, that are available to the console and API. If the ListRuns response doesn't include specific runs that you expected, you can find all run logs in the CloudWatch logs. For more information about viewing the run logs, see CloudWatch logs in the Amazon Web Services HealthOmics User Guide.

Retrieves a list of sequence stores.

Retrieves the resource shares associated with an account.

Use the filter parameter to retrieve a specific subset of the shares.

Retrieves a list of tags for a resource.

Retrieves a list of variant import jobs.

Retrieves a list of variant stores.

Lists the workflow versions for the specified workflow.

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

Retrieves a list of existing workflows.

You can filter for specific workflows by their name and type. Using the type parameter, specify PRIVATE to retrieve a list of private workflows or specify READY2RUN for a list of all Ready2Run workflows. If you do not specify the type of workflow, this operation returns a list of existing workflows.

Adds an access policy to the specified store.

Starts an annotation import job.

Activates an archived read set.

To reduce storage charges, Amazon Omics archives unused read sets after 30 days.

Exports a read set to Amazon S3.

Starts a read set import job.

Starts a reference import job.

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 GetRun 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 GetRun 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.

StartRun 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 StartRun, 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.

Starts a variant import job.

Tags a resource.

Removes tags from a resource.

Updates an annotation store.

Updates the description of an annotation store version.

Updates a run cache using its ID and returns a response with no body if the operation is successful.

You can update the run cache description, name, or the default run cache behavior with CACHE_ON_FAILURE or CACHE_ALWAYS. To confirm that your run cache settings have been properly updated, use the GetRunCache API operation.

For more information, see How call caching works in the Amazon Web Services HealthOmics User Guide.

Updates the settings of a run group and returns a response with no body if the operation is successful.

You can update the following settings with UpdateRunGroup:

• Maximum number of CPUs

• Run time (measured in minutes)

• Number of GPUs

• Number of concurrent runs

• Group name

To confirm that the settings have been successfully updated, use the ListRunGroups or GetRunGroup API operations to verify that the desired changes have been made.

Update one or more parameters for the sequence store.

Updates a variant store.

Updates information about a workflow.

You can update the following workflow information:

• Name

• Description

• Default storage type

• Default storage capacity (with workflow ID)

This operation returns a response with no body if the operation is successful. You can check the workflow updates by calling the GetWorkflow API operation.

For more information, see Update a private workflow in the Amazon Web Services HealthOmics User Guide.

Updates information about the workflow version.

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

This operation uploads a specific part of a read set.

If you upload a new part using a previously used part number, the previously uploaded part will be overwritten.