AbortMultipartReadSetUpload

$result = $client->abortMultipartReadSetUpload([/* ... */]);
$promise = $client->abortMultipartReadSetUploadAsync([/* ... */]);

Stops a multipart read set upload into a sequence store and returns a response with no body if the operation is successful. To confirm that a multipart read set upload has been stopped, use the ListMultipartReadSetUploads API operation to view all active multipart read set uploads.

Parameter Syntax

$result = $client->abortMultipartReadSetUpload([
    'sequenceStoreId' => '<string>', // REQUIRED
    'uploadId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

NotSupportedOperationException:

The operation is not supported by Amazon Omics, or the API does not exist.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

AcceptShare

$result = $client->acceptShare([/* ... */]);
$promise = $client->acceptShareAsync([/* ... */]);

Accept a resource share request.

Parameter Syntax

$result = $client->acceptShare([
    'shareId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'status' => 'PENDING|ACTIVATING|ACTIVE|DELETING|DELETED|FAILED',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

BatchDeleteReadSet

$result = $client->batchDeleteReadSet([/* ... */]);
$promise = $client->batchDeleteReadSetAsync([/* ... */]);

Deletes one or more read sets. If the operation is successful, it returns a response with no body. If there is an error with deleting one of the read sets, the operation returns an error list. If the operation successfully deletes only a subset of files, it will return an error list for the remaining files that fail to be deleted. There is a limit of 100 read sets that can be deleted in each BatchDeleteReadSet API call.

Parameter Syntax

$result = $client->batchDeleteReadSet([
    'ids' => ['<string>', ...], // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'errors' => [
        [
            'code' => '<string>',
            'id' => '<string>',
            'message' => '<string>',
        ],
        // ...
    ],
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

CancelAnnotationImportJob

$result = $client->cancelAnnotationImportJob([/* ... */]);
$promise = $client->cancelAnnotationImportJobAsync([/* ... */]);

Cancels an annotation import job.

Parameter Syntax

$result = $client->cancelAnnotationImportJob([
    'jobId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

CancelRun

$result = $client->cancelRun([/* ... */]);
$promise = $client->cancelRunAsync([/* ... */]);

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.

Parameter Syntax

$result = $client->cancelRun([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

CancelVariantImportJob

$result = $client->cancelVariantImportJob([/* ... */]);
$promise = $client->cancelVariantImportJobAsync([/* ... */]);

Cancels a variant import job.

Parameter Syntax

$result = $client->cancelVariantImportJob([
    'jobId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

CompleteMultipartReadSetUpload

$result = $client->completeMultipartReadSetUpload([/* ... */]);
$promise = $client->completeMultipartReadSetUploadAsync([/* ... */]);

Completes a multipart read set upload into a sequence store after you have initiated the upload process with CreateMultipartReadSetUpload and uploaded all read set parts using UploadReadSetPart. You must specify the parts you uploaded using the parts parameter. If the operation is successful, it returns the read set ID(s) of the uploaded read set(s).

For more information, see Direct upload to a sequence store in the Amazon Web Services HealthOmics User Guide.

Parameter Syntax

$result = $client->completeMultipartReadSetUpload([
    'parts' => [ // REQUIRED
        [
            'checksum' => '<string>', // REQUIRED
            'partNumber' => <integer>, // REQUIRED
            'partSource' => 'SOURCE1|SOURCE2', // REQUIRED
        ],
        // ...
    ],
    'sequenceStoreId' => '<string>', // REQUIRED
    'uploadId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'readSetId' => '<string>',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

NotSupportedOperationException:

The operation is not supported by Amazon Omics, or the API does not exist.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

CreateAnnotationStore

$result = $client->createAnnotationStore([/* ... */]);
$promise = $client->createAnnotationStoreAsync([/* ... */]);

Creates an annotation store.

Parameter Syntax

$result = $client->createAnnotationStore([
    'description' => '<string>',
    'name' => '<string>',
    'reference' => [
        'referenceArn' => '<string>',
    ],
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS', // REQUIRED
    ],
    'storeFormat' => 'GFF|TSV|VCF', // REQUIRED
    'storeOptions' => [
        'tsvStoreOptions' => [
            'annotationType' => 'GENERIC|CHR_POS|CHR_POS_REF_ALT|CHR_START_END_ONE_BASE|CHR_START_END_REF_ALT_ONE_BASE|CHR_START_END_ZERO_BASE|CHR_START_END_REF_ALT_ZERO_BASE',
            'formatToHeader' => ['<string>', ...],
            'schema' => [
                ['<string>', ...],
                // ...
            ],
        ],
    ],
    'tags' => ['<string>', ...],
    'versionName' => '<string>',
]);

Parameter Details

Result Syntax

[
    'creationTime' => <DateTime>,
    'id' => '<string>',
    'name' => '<string>',
    'reference' => [
        'referenceArn' => '<string>',
    ],
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
    'storeFormat' => 'GFF|TSV|VCF',
    'storeOptions' => [
        'tsvStoreOptions' => [
            'annotationType' => 'GENERIC|CHR_POS|CHR_POS_REF_ALT|CHR_START_END_ONE_BASE|CHR_START_END_REF_ALT_ONE_BASE|CHR_START_END_ZERO_BASE|CHR_START_END_REF_ALT_ZERO_BASE',
            'formatToHeader' => ['<string>', ...],
            'schema' => [
                ['<string>', ...],
                // ...
            ],
        ],
    ],
    'versionName' => '<string>',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

CreateAnnotationStoreVersion

$result = $client->createAnnotationStoreVersion([/* ... */]);
$promise = $client->createAnnotationStoreVersionAsync([/* ... */]);

Creates a new version of an annotation store.

Parameter Syntax

$result = $client->createAnnotationStoreVersion([
    'description' => '<string>',
    'name' => '<string>', // REQUIRED
    'tags' => ['<string>', ...],
    'versionName' => '<string>', // REQUIRED
    'versionOptions' => [
        'tsvVersionOptions' => [
            'annotationType' => 'GENERIC|CHR_POS|CHR_POS_REF_ALT|CHR_START_END_ONE_BASE|CHR_START_END_REF_ALT_ONE_BASE|CHR_START_END_ZERO_BASE|CHR_START_END_REF_ALT_ZERO_BASE',
            'formatToHeader' => ['<string>', ...],
            'schema' => [
                ['<string>', ...],
                // ...
            ],
        ],
    ],
]);

Parameter Details

Result Syntax

[
    'creationTime' => <DateTime>,
    'id' => '<string>',
    'name' => '<string>',
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
    'storeId' => '<string>',
    'versionName' => '<string>',
    'versionOptions' => [
        'tsvVersionOptions' => [
            'annotationType' => 'GENERIC|CHR_POS|CHR_POS_REF_ALT|CHR_START_END_ONE_BASE|CHR_START_END_REF_ALT_ONE_BASE|CHR_START_END_ZERO_BASE|CHR_START_END_REF_ALT_ZERO_BASE',
            'formatToHeader' => ['<string>', ...],
            'schema' => [
                ['<string>', ...],
                // ...
            ],
        ],
    ],
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

CreateMultipartReadSetUpload

$result = $client->createMultipartReadSetUpload([/* ... */]);
$promise = $client->createMultipartReadSetUploadAsync([/* ... */]);

Initiates a multipart read set upload for uploading partitioned source files into a sequence store. You can directly import source files from an EC2 instance and other local compute, or from an S3 bucket. To separate these source files into parts, use the split operation. Each part cannot be larger than 100 MB. If the operation is successful, it provides an uploadId which is required by the UploadReadSetPart API operation to upload parts into a sequence store.

To continue uploading a multipart read set into your sequence store, you must use the UploadReadSetPart API operation to upload each part individually following the steps below:

• Specify the uploadId obtained from the previous call to CreateMultipartReadSetUpload.

• Upload parts for that uploadId.

When you have finished uploading parts, use the CompleteMultipartReadSetUpload API to complete the multipart read set upload and to retrieve the final read set IDs in the response.

To learn more about creating parts and the split operation, see Direct upload to a sequence store in the Amazon Web Services HealthOmics User Guide.

Parameter Syntax

$result = $client->createMultipartReadSetUpload([
    'clientToken' => '<string>',
    'description' => '<string>',
    'generatedFrom' => '<string>',
    'name' => '<string>', // REQUIRED
    'referenceArn' => '<string>',
    'sampleId' => '<string>', // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
    'sourceFileType' => 'FASTQ|BAM|CRAM|UBAM', // REQUIRED
    'subjectId' => '<string>', // REQUIRED
    'tags' => ['<string>', ...],
]);

Parameter Details

Result Syntax

[
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'generatedFrom' => '<string>',
    'name' => '<string>',
    'referenceArn' => '<string>',
    'sampleId' => '<string>',
    'sequenceStoreId' => '<string>',
    'sourceFileType' => 'FASTQ|BAM|CRAM|UBAM',
    'subjectId' => '<string>',
    'tags' => ['<string>', ...],
    'uploadId' => '<string>',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

NotSupportedOperationException:

The operation is not supported by Amazon Omics, or the API does not exist.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

CreateReferenceStore

$result = $client->createReferenceStore([/* ... */]);
$promise = $client->createReferenceStoreAsync([/* ... */]);

Creates a reference store and returns metadata in JSON format. Reference stores are used to store reference genomes in FASTA format. A reference store is created when the first reference genome is imported. To import additional reference genomes from an Amazon S3 bucket, use the StartReferenceImportJob API operation.

For more information, see Creating a HealthOmics reference store in the Amazon Web Services HealthOmics User Guide.

Parameter Syntax

$result = $client->createReferenceStore([
    'clientToken' => '<string>',
    'description' => '<string>',
    'name' => '<string>', // REQUIRED
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS', // REQUIRED
    ],
    'tags' => ['<string>', ...],
]);

Parameter Details

Result Syntax

[
    'arn' => '<string>',
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'id' => '<string>',
    'name' => '<string>',
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS',
    ],
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

CreateRunCache

$result = $client->createRunCache([/* ... */]);
$promise = $client->createRunCacheAsync([/* ... */]);

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.

Parameter Syntax

$result = $client->createRunCache([
    'cacheBehavior' => 'CACHE_ON_FAILURE|CACHE_ALWAYS',
    'cacheBucketOwnerId' => '<string>',
    'cacheS3Location' => '<string>', // REQUIRED
    'description' => '<string>',
    'name' => '<string>',
    'requestId' => '<string>', // REQUIRED
    'tags' => ['<string>', ...],
]);

Parameter Details

Result Syntax

[
    'arn' => '<string>',
    'id' => '<string>',
    'status' => 'ACTIVE|DELETED|FAILED',
    'tags' => ['<string>', ...],
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

CreateRunGroup

$result = $client->createRunGroup([/* ... */]);
$promise = $client->createRunGroupAsync([/* ... */]);

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.

Parameter Syntax

$result = $client->createRunGroup([
    'maxCpus' => <integer>,
    'maxDuration' => <integer>,
    'maxGpus' => <integer>,
    'maxRuns' => <integer>,
    'name' => '<string>',
    'requestId' => '<string>', // REQUIRED
    'tags' => ['<string>', ...],
]);

Parameter Details

Result Syntax

[
    'arn' => '<string>',
    'id' => '<string>',
    'tags' => ['<string>', ...],
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

CreateSequenceStore

$result = $client->createSequenceStore([/* ... */]);
$promise = $client->createSequenceStoreAsync([/* ... */]);

Creates a sequence store and returns its metadata. Sequence stores are used to store sequence data files called read sets that are saved in FASTQ, BAM, uBAM, or CRAM formats. For aligned formats (BAM and CRAM), a sequence store can only use one reference genome. For unaligned formats (FASTQ and uBAM), a reference genome is not required. You can create multiple sequence stores per region per account.

The following are optional parameters you can specify for your sequence store:

• Use s3AccessConfig to configure your sequence store with S3 access logs (recommended).

• Use sseConfig to define your own KMS key for encryption.

• Use eTagAlgorithmFamily to define which algorithm to use for the HealthOmics eTag on objects.

• Use fallbackLocation to define a backup location for storing files that have failed a direct upload.

• Use propagatedSetLevelTags to configure tags that propagate to all objects in your store.

For more information, see Creating a HealthOmics sequence store in the Amazon Web Services HealthOmics User Guide.

Parameter Syntax

$result = $client->createSequenceStore([
    'clientToken' => '<string>',
    'description' => '<string>',
    'eTagAlgorithmFamily' => 'MD5up|SHA256up|SHA512up',
    'fallbackLocation' => '<string>',
    'name' => '<string>', // REQUIRED
    'propagatedSetLevelTags' => ['<string>', ...],
    's3AccessConfig' => [
        'accessLogLocation' => '<string>',
    ],
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS', // REQUIRED
    ],
    'tags' => ['<string>', ...],
]);

Parameter Details

Result Syntax

[
    'arn' => '<string>',
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'eTagAlgorithmFamily' => 'MD5up|SHA256up|SHA512up',
    'fallbackLocation' => '<string>',
    'id' => '<string>',
    'name' => '<string>',
    'propagatedSetLevelTags' => ['<string>', ...],
    's3Access' => [
        'accessLogLocation' => '<string>',
        's3AccessPointArn' => '<string>',
        's3Uri' => '<string>',
    ],
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS',
    ],
    'status' => 'CREATING|ACTIVE|UPDATING|DELETING|FAILED',
    'statusMessage' => '<string>',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

CreateShare

$result = $client->createShare([/* ... */]);
$promise = $client->createShareAsync([/* ... */]);

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

Parameter Syntax

$result = $client->createShare([
    'principalSubscriber' => '<string>', // REQUIRED
    'resourceArn' => '<string>', // REQUIRED
    'shareName' => '<string>',
]);

Parameter Details

Result Syntax

[
    'shareId' => '<string>',
    'shareName' => '<string>',
    'status' => 'PENDING|ACTIVATING|ACTIVE|DELETING|DELETED|FAILED',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

CreateVariantStore

$result = $client->createVariantStore([/* ... */]);
$promise = $client->createVariantStoreAsync([/* ... */]);

Creates a variant store.

Parameter Syntax

$result = $client->createVariantStore([
    'description' => '<string>',
    'name' => '<string>',
    'reference' => [ // REQUIRED
        'referenceArn' => '<string>',
    ],
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS', // REQUIRED
    ],
    'tags' => ['<string>', ...],
]);

Parameter Details

Result Syntax

[
    'creationTime' => <DateTime>,
    'id' => '<string>',
    'name' => '<string>',
    'reference' => [
        'referenceArn' => '<string>',
    ],
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

CreateWorkflow

$result = $client->createWorkflow([/* ... */]);
$promise = $client->createWorkflowAsync([/* ... */]);

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 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 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.

Parameter Syntax

$result = $client->createWorkflow([
    'accelerators' => 'GPU',
    'containerRegistryMap' => [
        'imageMappings' => [
            [
                'destinationImage' => '<string>',
                'sourceImage' => '<string>',
            ],
            // ...
        ],
        'registryMappings' => [
            [
                'ecrAccountId' => '<string>',
                'ecrRepositoryPrefix' => '<string>',
                'upstreamRegistryUrl' => '<string>',
                'upstreamRepositoryPrefix' => '<string>',
            ],
            // ...
        ],
    ],
    'containerRegistryMapUri' => '<string>',
    'definitionRepository' => [
        'connectionArn' => '<string>', // REQUIRED
        'excludeFilePatterns' => ['<string>', ...],
        'fullRepositoryId' => '<string>', // REQUIRED
        'sourceReference' => [
            'type' => 'BRANCH|TAG|COMMIT', // REQUIRED
            'value' => '<string>', // REQUIRED
        ],
    ],
    'definitionUri' => '<string>',
    'definitionZip' => <string || resource || Psr\Http\Message\StreamInterface>,
    'description' => '<string>',
    'engine' => 'WDL|NEXTFLOW|CWL',
    'main' => '<string>',
    'name' => '<string>',
    'parameterTemplate' => [
        '<WorkflowParameterName>' => [
            'description' => '<string>',
            'optional' => true || false,
        ],
        // ...
    ],
    'parameterTemplatePath' => '<string>',
    'readmeMarkdown' => '<string>',
    'readmePath' => '<string>',
    'readmeUri' => '<string>',
    'requestId' => '<string>', // REQUIRED
    'storageCapacity' => <integer>,
    'storageType' => 'STATIC|DYNAMIC',
    'tags' => ['<string>', ...],
    'workflowBucketOwnerId' => '<string>',
]);

Parameter Details

Result Syntax

[
    'arn' => '<string>',
    'id' => '<string>',
    'status' => 'CREATING|ACTIVE|UPDATING|DELETED|FAILED|INACTIVE',
    'tags' => ['<string>', ...],
    'uuid' => '<string>',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

CreateWorkflowVersion

$result = $client->createWorkflowVersion([/* ... */]);
$promise = $client->createWorkflowVersionAsync([/* ... */]);

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.

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

Parameter Syntax

$result = $client->createWorkflowVersion([
    'accelerators' => 'GPU',
    'containerRegistryMap' => [
        'imageMappings' => [
            [
                'destinationImage' => '<string>',
                'sourceImage' => '<string>',
            ],
            // ...
        ],
        'registryMappings' => [
            [
                'ecrAccountId' => '<string>',
                'ecrRepositoryPrefix' => '<string>',
                'upstreamRegistryUrl' => '<string>',
                'upstreamRepositoryPrefix' => '<string>',
            ],
            // ...
        ],
    ],
    'containerRegistryMapUri' => '<string>',
    'definitionRepository' => [
        'connectionArn' => '<string>', // REQUIRED
        'excludeFilePatterns' => ['<string>', ...],
        'fullRepositoryId' => '<string>', // REQUIRED
        'sourceReference' => [
            'type' => 'BRANCH|TAG|COMMIT', // REQUIRED
            'value' => '<string>', // REQUIRED
        ],
    ],
    'definitionUri' => '<string>',
    'definitionZip' => <string || resource || Psr\Http\Message\StreamInterface>,
    'description' => '<string>',
    'engine' => 'WDL|NEXTFLOW|CWL',
    'main' => '<string>',
    'parameterTemplate' => [
        '<WorkflowParameterName>' => [
            'description' => '<string>',
            'optional' => true || false,
        ],
        // ...
    ],
    'parameterTemplatePath' => '<string>',
    'readmeMarkdown' => '<string>',
    'readmePath' => '<string>',
    'readmeUri' => '<string>',
    'requestId' => '<string>', // REQUIRED
    'storageCapacity' => <integer>,
    'storageType' => 'STATIC|DYNAMIC',
    'tags' => ['<string>', ...],
    'versionName' => '<string>', // REQUIRED
    'workflowBucketOwnerId' => '<string>',
    'workflowId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'arn' => '<string>',
    'status' => 'CREATING|ACTIVE|UPDATING|DELETED|FAILED|INACTIVE',
    'tags' => ['<string>', ...],
    'uuid' => '<string>',
    'versionName' => '<string>',
    'workflowId' => '<string>',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

DeleteAnnotationStore

$result = $client->deleteAnnotationStore([/* ... */]);
$promise = $client->deleteAnnotationStoreAsync([/* ... */]);

Deletes an annotation store.

Parameter Syntax

$result = $client->deleteAnnotationStore([
    'force' => true || false,
    'name' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

DeleteAnnotationStoreVersions

$result = $client->deleteAnnotationStoreVersions([/* ... */]);
$promise = $client->deleteAnnotationStoreVersionsAsync([/* ... */]);

Deletes one or multiple versions of an annotation store.

Parameter Syntax

$result = $client->deleteAnnotationStoreVersions([
    'force' => true || false,
    'name' => '<string>', // REQUIRED
    'versions' => ['<string>', ...], // REQUIRED
]);

Parameter Details

Result Syntax

[
    'errors' => [
        [
            'message' => '<string>',
            'versionName' => '<string>',
        ],
        // ...
    ],
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

DeleteReference

$result = $client->deleteReference([/* ... */]);
$promise = $client->deleteReferenceAsync([/* ... */]);

Deletes a reference genome and returns a response with no body if the operation is successful. The read set associated with the reference genome must first be deleted before deleting the reference genome. After the reference genome is deleted, you can delete the reference store using the DeleteReferenceStore API operation.

For more information, see Deleting HealthOmics reference and sequence stores in the Amazon Web Services HealthOmics User Guide.

Parameter Syntax

$result = $client->deleteReference([
    'id' => '<string>', // REQUIRED
    'referenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

DeleteReferenceStore

$result = $client->deleteReferenceStore([/* ... */]);
$promise = $client->deleteReferenceStoreAsync([/* ... */]);

Deletes a reference store and returns a response with no body if the operation is successful. You can only delete a reference store when it does not contain any reference genomes. To empty a reference store, use DeleteReference.

For more information about your workflow status, see Deleting HealthOmics reference and sequence stores in the Amazon Web Services HealthOmics User Guide.

Parameter Syntax

$result = $client->deleteReferenceStore([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

DeleteRun

$result = $client->deleteRun([/* ... */]);
$promise = $client->deleteRunAsync([/* ... */]);

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.

Parameter Syntax

$result = $client->deleteRun([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

DeleteRunCache

$result = $client->deleteRunCache([/* ... */]);
$promise = $client->deleteRunCacheAsync([/* ... */]);

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.

Parameter Syntax

$result = $client->deleteRunCache([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

DeleteRunGroup

$result = $client->deleteRunGroup([/* ... */]);
$promise = $client->deleteRunGroupAsync([/* ... */]);

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.

Parameter Syntax

$result = $client->deleteRunGroup([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

DeleteS3AccessPolicy

$result = $client->deleteS3AccessPolicy([/* ... */]);
$promise = $client->deleteS3AccessPolicyAsync([/* ... */]);

Deletes an access policy for the specified store.

Parameter Syntax

$result = $client->deleteS3AccessPolicy([
    's3AccessPointArn' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[]

Result Details

Errors

NotSupportedOperationException:

The operation is not supported by Amazon Omics, or the API does not exist.

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

DeleteSequenceStore

$result = $client->deleteSequenceStore([/* ... */]);
$promise = $client->deleteSequenceStoreAsync([/* ... */]);

Deletes a sequence store and returns a response with no body if the operation is successful. You can only delete a sequence store when it does not contain any read sets.

Use the BatchDeleteReadSet API operation to ensure that all read sets in the sequence store are deleted. When a sequence store is deleted, all tags associated with the store are also deleted.

For more information, see Deleting HealthOmics reference and sequence stores in the Amazon Web Services HealthOmics User Guide.

Parameter Syntax

$result = $client->deleteSequenceStore([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

DeleteShare

$result = $client->deleteShare([/* ... */]);
$promise = $client->deleteShareAsync([/* ... */]);

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.

Parameter Syntax

$result = $client->deleteShare([
    'shareId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'status' => 'PENDING|ACTIVATING|ACTIVE|DELETING|DELETED|FAILED',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

DeleteVariantStore

$result = $client->deleteVariantStore([/* ... */]);
$promise = $client->deleteVariantStoreAsync([/* ... */]);

Deletes a variant store.

Parameter Syntax

$result = $client->deleteVariantStore([
    'force' => true || false,
    'name' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

DeleteWorkflow

$result = $client->deleteWorkflow([/* ... */]);
$promise = $client->deleteWorkflowAsync([/* ... */]);

Deletes a workflow by specifying its ID. This operation returns a response with no body 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.

Parameter Syntax

$result = $client->deleteWorkflow([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

DeleteWorkflowVersion

$result = $client->deleteWorkflowVersion([/* ... */]);
$promise = $client->deleteWorkflowVersionAsync([/* ... */]);

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.

Parameter Syntax

$result = $client->deleteWorkflowVersion([
    'versionName' => '<string>', // REQUIRED
    'workflowId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ServiceQuotaExceededException:

The request exceeds a service quota.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetAnnotationImportJob

$result = $client->getAnnotationImportJob([/* ... */]);
$promise = $client->getAnnotationImportJobAsync([/* ... */]);

Gets information about an annotation import job.

Parameter Syntax

$result = $client->getAnnotationImportJob([
    'jobId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'annotationFields' => ['<string>', ...],
    'completionTime' => <DateTime>,
    'creationTime' => <DateTime>,
    'destinationName' => '<string>',
    'formatOptions' => [
        'tsvOptions' => [
            'readOptions' => [
                'comment' => '<string>',
                'encoding' => '<string>',
                'escape' => '<string>',
                'escapeQuotes' => true || false,
                'header' => true || false,
                'lineSep' => '<string>',
                'quote' => '<string>',
                'quoteAll' => true || false,
                'sep' => '<string>',
            ],
        ],
        'vcfOptions' => [
            'ignoreFilterField' => true || false,
            'ignoreQualField' => true || false,
        ],
    ],
    'id' => '<string>',
    'items' => [
        [
            'jobStatus' => 'SUBMITTED|IN_PROGRESS|CANCELLED|COMPLETED|FAILED|COMPLETED_WITH_FAILURES',
            'source' => '<string>',
        ],
        // ...
    ],
    'roleArn' => '<string>',
    'runLeftNormalization' => true || false,
    'status' => 'SUBMITTED|IN_PROGRESS|CANCELLED|COMPLETED|FAILED|COMPLETED_WITH_FAILURES',
    'statusMessage' => '<string>',
    'updateTime' => <DateTime>,
    'versionName' => '<string>',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

GetAnnotationStore

$result = $client->getAnnotationStore([/* ... */]);
$promise = $client->getAnnotationStoreAsync([/* ... */]);

Gets information about an annotation store.

Parameter Syntax

$result = $client->getAnnotationStore([
    'name' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'id' => '<string>',
    'name' => '<string>',
    'numVersions' => <integer>,
    'reference' => [
        'referenceArn' => '<string>',
    ],
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS',
    ],
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
    'statusMessage' => '<string>',
    'storeArn' => '<string>',
    'storeFormat' => 'GFF|TSV|VCF',
    'storeOptions' => [
        'tsvStoreOptions' => [
            'annotationType' => 'GENERIC|CHR_POS|CHR_POS_REF_ALT|CHR_START_END_ONE_BASE|CHR_START_END_REF_ALT_ONE_BASE|CHR_START_END_ZERO_BASE|CHR_START_END_REF_ALT_ZERO_BASE',
            'formatToHeader' => ['<string>', ...],
            'schema' => [
                ['<string>', ...],
                // ...
            ],
        ],
    ],
    'storeSizeBytes' => <integer>,
    'tags' => ['<string>', ...],
    'updateTime' => <DateTime>,
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

GetAnnotationStoreVersion

$result = $client->getAnnotationStoreVersion([/* ... */]);
$promise = $client->getAnnotationStoreVersionAsync([/* ... */]);

Retrieves the metadata for an annotation store version.

Parameter Syntax

$result = $client->getAnnotationStoreVersion([
    'name' => '<string>', // REQUIRED
    'versionName' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'id' => '<string>',
    'name' => '<string>',
    'status' => 'CREATING|UPDATING|DELETING|ACTIVE|FAILED',
    'statusMessage' => '<string>',
    'storeId' => '<string>',
    'tags' => ['<string>', ...],
    'updateTime' => <DateTime>,
    'versionArn' => '<string>',
    'versionName' => '<string>',
    'versionOptions' => [
        'tsvVersionOptions' => [
            'annotationType' => 'GENERIC|CHR_POS|CHR_POS_REF_ALT|CHR_START_END_ONE_BASE|CHR_START_END_REF_ALT_ONE_BASE|CHR_START_END_ZERO_BASE|CHR_START_END_REF_ALT_ZERO_BASE',
            'formatToHeader' => ['<string>', ...],
            'schema' => [
                ['<string>', ...],
                // ...
            ],
        ],
    ],
    'versionSizeBytes' => <integer>,
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

GetReadSet

$result = $client->getReadSet([/* ... */]);
$promise = $client->getReadSetAsync([/* ... */]);

Retrieves detailed information from parts of a read set and returns the read set in the same format that it was uploaded. You must have read sets uploaded to your sequence store in order to run this operation.

Parameter Syntax

$result = $client->getReadSet([
    'file' => 'SOURCE1|SOURCE2|INDEX',
    'id' => '<string>', // REQUIRED
    'partNumber' => <integer>, // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'payload' => <string || resource || Psr\Http\Message\StreamInterface>,
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

RangeNotSatisfiableException:

The ranges specified in the request are not valid.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ConflictException:

The request cannot be applied to the target resource in its current state.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetReadSetActivationJob

$result = $client->getReadSetActivationJob([/* ... */]);
$promise = $client->getReadSetActivationJobAsync([/* ... */]);

Returns detailed information about the status of a read set activation job in JSON format.

Parameter Syntax

$result = $client->getReadSetActivationJob([
    'id' => '<string>', // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'completionTime' => <DateTime>,
    'creationTime' => <DateTime>,
    'id' => '<string>',
    'sequenceStoreId' => '<string>',
    'sources' => [
        [
            'readSetId' => '<string>',
            'status' => 'NOT_STARTED|IN_PROGRESS|FINISHED|FAILED',
            'statusMessage' => '<string>',
        ],
        // ...
    ],
    'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
    'statusMessage' => '<string>',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetReadSetExportJob

$result = $client->getReadSetExportJob([/* ... */]);
$promise = $client->getReadSetExportJobAsync([/* ... */]);

Retrieves status information about a read set export job and returns the data in JSON format. Use this operation to actively monitor the progress of an export job.

Parameter Syntax

$result = $client->getReadSetExportJob([
    'id' => '<string>', // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'completionTime' => <DateTime>,
    'creationTime' => <DateTime>,
    'destination' => '<string>',
    'id' => '<string>',
    'readSets' => [
        [
            'id' => '<string>',
            'status' => 'NOT_STARTED|IN_PROGRESS|FINISHED|FAILED',
            'statusMessage' => '<string>',
        ],
        // ...
    ],
    'sequenceStoreId' => '<string>',
    'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
    'statusMessage' => '<string>',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetReadSetImportJob

$result = $client->getReadSetImportJob([/* ... */]);
$promise = $client->getReadSetImportJobAsync([/* ... */]);

Gets detailed and status information about a read set import job and returns the data in JSON format.

Parameter Syntax

$result = $client->getReadSetImportJob([
    'id' => '<string>', // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'completionTime' => <DateTime>,
    'creationTime' => <DateTime>,
    'id' => '<string>',
    'roleArn' => '<string>',
    'sequenceStoreId' => '<string>',
    'sources' => [
        [
            'description' => '<string>',
            'generatedFrom' => '<string>',
            'name' => '<string>',
            'readSetId' => '<string>',
            'referenceArn' => '<string>',
            'sampleId' => '<string>',
            'sourceFileType' => 'FASTQ|BAM|CRAM|UBAM',
            'sourceFiles' => [
                'source1' => '<string>',
                'source2' => '<string>',
            ],
            'status' => 'NOT_STARTED|IN_PROGRESS|FINISHED|FAILED',
            'statusMessage' => '<string>',
            'subjectId' => '<string>',
            'tags' => ['<string>', ...],
        ],
        // ...
    ],
    'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
    'statusMessage' => '<string>',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetReadSetMetadata

$result = $client->getReadSetMetadata([/* ... */]);
$promise = $client->getReadSetMetadataAsync([/* ... */]);

Retrieves the metadata for a read set from a sequence store in JSON format. This operation does not return tags. To retrieve the list of tags for a read set, use the ListTagsForResource API operation.

Parameter Syntax

$result = $client->getReadSetMetadata([
    'id' => '<string>', // REQUIRED
    'sequenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'arn' => '<string>',
    'creationJobId' => '<string>',
    'creationTime' => <DateTime>,
    'creationType' => 'IMPORT|UPLOAD',
    'description' => '<string>',
    'etag' => [
        'algorithm' => 'FASTQ_MD5up|BAM_MD5up|CRAM_MD5up|FASTQ_SHA256up|BAM_SHA256up|CRAM_SHA256up|FASTQ_SHA512up|BAM_SHA512up|CRAM_SHA512up',
        'source1' => '<string>',
        'source2' => '<string>',
    ],
    'fileType' => 'FASTQ|BAM|CRAM|UBAM',
    'files' => [
        'index' => [
            'contentLength' => <integer>,
            'partSize' => <integer>,
            's3Access' => [
                's3Uri' => '<string>',
            ],
            'totalParts' => <integer>,
        ],
        'source1' => [
            'contentLength' => <integer>,
            'partSize' => <integer>,
            's3Access' => [
                's3Uri' => '<string>',
            ],
            'totalParts' => <integer>,
        ],
        'source2' => [
            'contentLength' => <integer>,
            'partSize' => <integer>,
            's3Access' => [
                's3Uri' => '<string>',
            ],
            'totalParts' => <integer>,
        ],
    ],
    'id' => '<string>',
    'name' => '<string>',
    'referenceArn' => '<string>',
    'sampleId' => '<string>',
    'sequenceInformation' => [
        'alignment' => '<string>',
        'generatedFrom' => '<string>',
        'totalBaseCount' => <integer>,
        'totalReadCount' => <integer>,
    ],
    'sequenceStoreId' => '<string>',
    'status' => 'ARCHIVED|ACTIVATING|ACTIVE|DELETING|DELETED|PROCESSING_UPLOAD|UPLOAD_FAILED',
    'statusMessage' => '<string>',
    'subjectId' => '<string>',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetReference

$result = $client->getReference([/* ... */]);
$promise = $client->getReferenceAsync([/* ... */]);

Downloads parts of data from a reference genome and returns the reference file in the same format that it was uploaded.

For more information, see Creating a HealthOmics reference store in the Amazon Web Services HealthOmics User Guide.

Parameter Syntax

$result = $client->getReference([
    'file' => 'SOURCE|INDEX',
    'id' => '<string>', // REQUIRED
    'partNumber' => <integer>, // REQUIRED
    'range' => '<string>',
    'referenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'payload' => <string || resource || Psr\Http\Message\StreamInterface>,
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

RangeNotSatisfiableException:

The ranges specified in the request are not valid.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetReferenceImportJob

$result = $client->getReferenceImportJob([/* ... */]);
$promise = $client->getReferenceImportJobAsync([/* ... */]);

Monitors the status of a reference import job. This operation can be called after calling the StartReferenceImportJob operation.

Parameter Syntax

$result = $client->getReferenceImportJob([
    'id' => '<string>', // REQUIRED
    'referenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'completionTime' => <DateTime>,
    'creationTime' => <DateTime>,
    'id' => '<string>',
    'referenceStoreId' => '<string>',
    'roleArn' => '<string>',
    'sources' => [
        [
            'description' => '<string>',
            'name' => '<string>',
            'referenceId' => '<string>',
            'sourceFile' => '<string>',
            'status' => 'NOT_STARTED|IN_PROGRESS|FINISHED|FAILED',
            'statusMessage' => '<string>',
            'tags' => ['<string>', ...],
        ],
        // ...
    ],
    'status' => 'SUBMITTED|IN_PROGRESS|CANCELLING|CANCELLED|FAILED|COMPLETED|COMPLETED_WITH_FAILURES',
    'statusMessage' => '<string>',
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetReferenceMetadata

$result = $client->getReferenceMetadata([/* ... */]);
$promise = $client->getReferenceMetadataAsync([/* ... */]);

Retrieves metadata for a reference genome. This operation returns the number of parts, part size, and MD5 of an entire file. This operation does not return tags. To retrieve the list of tags for a read set, use the ListTagsForResource API operation.

Parameter Syntax

$result = $client->getReferenceMetadata([
    'id' => '<string>', // REQUIRED
    'referenceStoreId' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'arn' => '<string>',
    'creationJobId' => '<string>',
    'creationTime' => <DateTime>,
    'creationType' => 'IMPORT',
    'description' => '<string>',
    'files' => [
        'index' => [
            'contentLength' => <integer>,
            'partSize' => <integer>,
            's3Access' => [
                's3Uri' => '<string>',
            ],
            'totalParts' => <integer>,
        ],
        'source' => [
            'contentLength' => <integer>,
            'partSize' => <integer>,
            's3Access' => [
                's3Uri' => '<string>',
            ],
            'totalParts' => <integer>,
        ],
    ],
    'id' => '<string>',
    'md5' => '<string>',
    'name' => '<string>',
    'referenceStoreId' => '<string>',
    'status' => 'ACTIVE|DELETING|DELETED',
    'updateTime' => <DateTime>,
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetReferenceStore

$result = $client->getReferenceStore([/* ... */]);
$promise = $client->getReferenceStoreAsync([/* ... */]);

Gets information about a reference store.

Parameter Syntax

$result = $client->getReferenceStore([
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'arn' => '<string>',
    'creationTime' => <DateTime>,
    'description' => '<string>',
    'id' => '<string>',
    'name' => '<string>',
    'sseConfig' => [
        'keyArn' => '<string>',
        'type' => 'KMS',
    ],
]

Result Details

Errors

InternalServerException:

An unexpected error occurred. Try the request again.

ThrottlingException:

The request was denied due to request throttling.

ValidationException:

The input fails to satisfy the constraints specified by an AWS service.

ResourceNotFoundException:

The target resource was not found in the current Region.

AccessDeniedException:

You do not have sufficient access to perform this action.

RequestTimeoutException:

The request timed out.

GetRun

$result = $client->getRun([/* ... */]);
$promise = $client->getRunAsync([/* ... */]);

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.

Parameter Syntax

$result = $client->getRun([
    'export' => ['<string>', ...],
    'id' => '<string>', // REQUIRED
]);

Parameter Details

Result Syntax

[
    'accelerators' => 'GPU',
    'arn' => '<string>',
    'cacheBehavior' => 'CACHE_ON_FAILURE|CACHE_ALWAYS',
    'cacheId' => '<string>',
    'creationTime' => <DateTime>,
    'definition' => '<string>',
    'digest' => '<string>',
    'engineVersion' => '<string>',
    'failureReason' => '<string>',
    'id' => '<string>',
    'logLevel' => 'OFF|FATAL|ERROR|ALL',
    'logLocation' => [
        'engineLogStream' => '<string>',
        'runLogStream' => '<string>',
    ],
    'name' => '<string>',
    'outputUri' => '<string>',
    'parameters' => [
    ],
    'priority' => <integer>,
    'resourceDigests' => ['<string>', ...],
    'retentionMode' => 'RETAIN|REMOVE',
    'roleArn' => '<string>',
    'runGroupId' => '<string>',
    'runId' => '<string>',
    'runOutputUri' => '<string>',
    'startTime' => <DateTime>,
    'startedBy' => '<string>',
    'status' => 'PENDING|STARTING|RUNNING|STOPPING|COMPLETED|DELETED|CANCELLED|FAILED',
    'statusMessage' => '<string>',
    'stopTime' => <DateTime>,
    'storageCapacity' => <integer>,
    'storageType' => 'STATIC|DYNAMIC',
    'tags' => ['<string>', ...],
    'uuid' => '<string>',
    'workflowId' => '<string>',
    'workflowOwnerId' => '<string>',
    'workflowType' => 'PRIVATE|READY2RUN',
    'workflowUuid' => '<string>',
    'workflowVersionName' => '<string>',
]

Result Details