OmicsClient

This is the AWS HealthOmics API Reference. For an introduction to the service, see What is AWS HealthOmics?  in the AWS HealthOmics User Guide.

Installation

NPM
npm install @aws-sdk/client-omics
Yarn
yarn add @aws-sdk/client-omics
pnpm
pnpm add @aws-sdk/client-omics

OmicsClient Operations

Command
Summary
AbortMultipartReadSetUploadCommand

Stops a multipart upload.

AcceptShareCommand

Accept a resource share request.

BatchDeleteReadSetCommand

Deletes one or more read sets.

CancelAnnotationImportJobCommand

Cancels an annotation import job.

CancelRunCommand

Cancels a run.

CancelVariantImportJobCommand

Cancels a variant import job.

CompleteMultipartReadSetUploadCommand

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

CreateAnnotationStoreCommand

Creates an annotation store.

CreateAnnotationStoreVersionCommand

Creates a new version of an annotation store.

CreateMultipartReadSetUploadCommand

Begins a multipart read set upload.

CreateReferenceStoreCommand

Creates a reference store.

CreateRunCacheCommand

You can create a run cache to save the task outputs from completed tasks in a run for a private workflow. Subsequent runs use the task outputs from the cache, rather than computing the task outputs again. You specify an Amazon S3 location where HealthOmics saves the cached data. This data must be immediately accessible (not in an archived state).

For more information, see Creating a run cache  in the AWS HealthOmics User Guide.

CreateRunGroupCommand

You can optionally create a run group to limit the compute resources for the runs that you add to the group.

CreateSequenceStoreCommand

Creates a sequence store.

CreateShareCommand

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

CreateVariantStoreCommand

Creates a variant store.

CreateWorkflowCommand

Creates a workflow.

DeleteAnnotationStoreCommand

Deletes an annotation store.

DeleteAnnotationStoreVersionsCommand

Deletes one or multiple versions of an annotation store.

DeleteReferenceCommand

Deletes a genome reference.

DeleteReferenceStoreCommand

Deletes a genome reference store.

DeleteRunCacheCommand

Delete a run cache. This action removes the cache metadata stored in the service account, but doesn't 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 AWS HealthOmics User Guide.

DeleteRunCommand

Deletes a workflow run.

DeleteRunGroupCommand

Deletes a workflow run group.

DeleteS3AccessPolicyCommand

Deletes an access policy for the specified store.

DeleteSequenceStoreCommand

Deletes a sequence store.

DeleteShareCommand

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.

DeleteVariantStoreCommand

Deletes a variant store.

DeleteWorkflowCommand

Deletes a workflow.

GetAnnotationImportJobCommand

Gets information about an annotation import job.

GetAnnotationStoreCommand

Gets information about an annotation store.

GetAnnotationStoreVersionCommand

Retrieves the metadata for an annotation store version.

GetReadSetActivationJobCommand

Gets information about a read set activation job.

GetReadSetCommand

Gets a file from a read set.

GetReadSetExportJobCommand

Gets information about a read set export job.

GetReadSetImportJobCommand

Gets information about a read set import job.

GetReadSetMetadataCommand

Gets details about a read set.

GetReferenceCommand

Gets a reference file.

GetReferenceImportJobCommand

Gets information about a reference import job.

GetReferenceMetadataCommand

Gets information about a genome reference's metadata.

GetReferenceStoreCommand

Gets information about a reference store.

GetRunCacheCommand

Retrieve the details for the specified run cache.

For more information, see Call caching for HealthOmics runs  in the AWS HealthOmics User Guide.

GetRunCommand

Gets information about a workflow run.

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

HealthOmics stores a fixed number of runs that are available to the console and API. If GetRun doesn't return the requested run, you can find run logs for all runs in the CloudWatch logs. For more information about viewing the run logs, see CloudWatch logs  in the AWS HealthOmics User Guide.

GetRunGroupCommand

Gets information about a workflow run group.

GetRunTaskCommand

Gets information about a workflow run task.

GetS3AccessPolicyCommand

Retrieves details about an access policy on a given store.

GetSequenceStoreCommand

Gets information about a sequence store.

GetShareCommand

Retrieves the metadata for the specified resource share.

GetVariantImportJobCommand

Gets information about a variant import job.

GetVariantStoreCommand

Gets information about a variant store.

GetWorkflowCommand

Gets information about a workflow.

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

ListAnnotationImportJobsCommand

Retrieves a list of annotation import jobs.

ListAnnotationStoreVersionsCommand

Lists the versions of an annotation store.

ListAnnotationStoresCommand

Retrieves a list of annotation stores.

ListMultipartReadSetUploadsCommand

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.

ListReadSetActivationJobsCommand

Retrieves a list of read set activation jobs.

ListReadSetExportJobsCommand

Retrieves a list of read set export jobs.

ListReadSetImportJobsCommand

Retrieves a list of read set import jobs.

ListReadSetUploadPartsCommand

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

ListReadSetsCommand

Retrieves a list of read sets.

ListReferenceImportJobsCommand

Retrieves a list of reference import jobs.

ListReferenceStoresCommand

Retrieves a list of reference stores.

ListReferencesCommand

Retrieves a list of references.

ListRunCachesCommand

Retrieves a list of your run caches.

ListRunGroupsCommand

Retrieves a list of run groups.

ListRunTasksCommand

Retrieves a list of tasks for a run.

ListRunsCommand

Retrieves a list of runs.

HealthOmics stores a fixed number of runs that are available to the console and API. If the ListRuns response doesn't include specific runs that you expected, you can find run logs for all runs in the CloudWatch logs. For more information about viewing the run logs, see CloudWatch logs  in the AWS HealthOmics User Guide.

ListSequenceStoresCommand

Retrieves a list of sequence stores.

ListSharesCommand

Retrieves the resource shares associated with an account. Use the filter parameter to retrieve a specific subset of the shares.

ListTagsForResourceCommand

Retrieves a list of tags for a resource.

ListVariantImportJobsCommand

Retrieves a list of variant import jobs.

ListVariantStoresCommand

Retrieves a list of variant stores.

ListWorkflowsCommand

Retrieves a list of workflows.

PutS3AccessPolicyCommand

Adds an access policy to the specified store.

StartAnnotationImportJobCommand

Starts an annotation import job.

StartReadSetActivationJobCommand

Activates an archived read set. To reduce storage charges, Amazon Omics archives unused read sets after 30 days.

StartReadSetExportJobCommand

Exports a read set to Amazon S3.

StartReadSetImportJobCommand

Starts a read set import job.

StartReferenceImportJobCommand

Starts a reference import job.

StartRunCommand

Starts a workflow run. To duplicate a run, specify the run's ID and a role ARN. The remaining parameters are copied from the previous run.

StartRun will not support re-run for a workflow that is shared with you.

HealthOmics stores a fixed number of runs that are available to the console and API. By default, HealthOmics doesn't any remove any runs. If HealthOmics reaches the maximum number of runs, you must manually remove runs. To have older runs removed automatically, set the retention mode to REMOVE.

By default, the run uses STATIC storage. For STATIC storage, set the storageCapacity field. You can set the storage type to DYNAMIC. You do not set storageCapacity, because HealthOmics dynamically scales the storage up or down as required. For more information about static and dynamic storage, see Running workflows  in the AWS HealthOmics User Guide.

StartVariantImportJobCommand

Starts a variant import job.

TagResourceCommand

Tags a resource.

UntagResourceCommand

Removes tags from a resource.

UpdateAnnotationStoreCommand

Updates an annotation store.

UpdateAnnotationStoreVersionCommand

Updates the description of an annotation store version.

UpdateRunCacheCommand

Update a run cache.

UpdateRunGroupCommand

Updates a run group.

UpdateSequenceStoreCommand

Update one or more parameters for the sequence store.

UpdateVariantStoreCommand

Updates a variant store.

UpdateWorkflowCommand

Updates a workflow.

UploadReadSetPartCommand

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.

OmicsClient Configuration

Parameter
Type
Description
defaultsMode
Optional
DefaultsMode | Provider<DefaultsMode>
The @smithy/smithy-client#DefaultsMode that will be used to determine how certain default configuration options are resolved in the SDK.
disableHostPrefix
Optional
boolean
Disable dynamically changing the endpoint of the client based on the hostPrefix trait of an operation.
extensions
Optional
RuntimeExtension[]
Optional extensions
logger
Optional
Logger
Optional logger for logging debug/info/warn/error.
maxAttempts
Optional
number | Provider<number>
Value for how many times a request will be made at most in case of retry.
profile
Optional
string
Setting a client profile is similar to setting a value for the AWS_PROFILE environment variable. Setting a profile on a client in code only affects the single client instance, unlike AWS_PROFILE.When set, and only for environments where an AWS configuration file exists, fields configurable by this file will be retrieved from the specified profile within that file. Conflicting code configuration and environment variables will still have higher priority.For client credential resolution that involves checking the AWS configuration file, the client's profile (this value) will be used unless a different profile is set in the credential provider options.
region
Optional
string | Provider<string>
The AWS region to which this client will send requests
requestHandler
Optional
__HttpHandlerUserInput
The HTTP handler to use or its constructor options. Fetch in browser and Https in Nodejs.
retryMode
Optional
string | Provider<string>
Specifies which retry algorithm to use.
useDualstackEndpoint
Optional
boolean | Provider<boolean>
Enables IPv6/IPv4 dualstack endpoint.
useFipsEndpoint
Optional
boolean | Provider<boolean>
Enables FIPS compatible endpoints.
Additional config fields are described in the full configuration type: OmicsClientConfig