R/omics_operations.R

In paws.storage: 'Amazon Web Services' Storage Services

# This file is generated by make.paws. Please do not edit here.
#' @importFrom paws.common get_config new_operation new_request send_request
#' @include omics_service.R
NULL

#' Stops a multipart read set upload into a sequence store and returns a
#' response with no body if the operation is successful
#'
#' @description
#' 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 [`list_multipart_read_set_uploads`][omics_list_multipart_read_set_uploads] API operation to view all active multipart read set uploads.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_abort_multipart_read_set_upload/](https://www.paws-r-sdk.com/docs/omics_abort_multipart_read_set_upload/) for full documentation.
#'
#' @param sequenceStoreId [required] The sequence store ID for the store involved in the multipart upload.
#' @param uploadId [required] The ID for the multipart upload.
#'
#' @keywords internal
#'
#' @rdname omics_abort_multipart_read_set_upload
omics_abort_multipart_read_set_upload <- function(sequenceStoreId, uploadId) {
  op <- new_operation(
    name = "AbortMultipartReadSetUpload",
    http_method = "DELETE",
    http_path = "/sequencestore/{sequenceStoreId}/upload/{uploadId}/abort",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$abort_multipart_read_set_upload_input(sequenceStoreId = sequenceStoreId, uploadId = uploadId)
  output <- .omics$abort_multipart_read_set_upload_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$abort_multipart_read_set_upload <- omics_abort_multipart_read_set_upload

#' Accept a resource share request
#'
#' @description
#' Accept a resource share request.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_accept_share/](https://www.paws-r-sdk.com/docs/omics_accept_share/) for full documentation.
#'
#' @param shareId &#91;required&#93; The ID of the resource share.
#'
#' @keywords internal
#'
#' @rdname omics_accept_share
omics_accept_share <- function(shareId) {
  op <- new_operation(
    name = "AcceptShare",
    http_method = "POST",
    http_path = "/share/{shareId}",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$accept_share_input(shareId = shareId)
  output <- .omics$accept_share_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$accept_share <- omics_accept_share

#' Deletes one or more read sets
#'
#' @description
#' 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 [`batch_delete_read_set`][omics_batch_delete_read_set] API call.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_batch_delete_read_set/](https://www.paws-r-sdk.com/docs/omics_batch_delete_read_set/) for full documentation.
#'
#' @param ids &#91;required&#93; The read sets' IDs.
#' @param sequenceStoreId &#91;required&#93; The read sets' sequence store ID.
#'
#' @keywords internal
#'
#' @rdname omics_batch_delete_read_set
omics_batch_delete_read_set <- function(ids, sequenceStoreId) {
  op <- new_operation(
    name = "BatchDeleteReadSet",
    http_method = "POST",
    http_path = "/sequencestore/{sequenceStoreId}/readset/batch/delete",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$batch_delete_read_set_input(ids = ids, sequenceStoreId = sequenceStoreId)
  output <- .omics$batch_delete_read_set_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$batch_delete_read_set <- omics_batch_delete_read_set

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_cancel_annotation_import_job/](https://www.paws-r-sdk.com/docs/omics_cancel_annotation_import_job/) for full documentation.
#'
#' @param jobId &#91;required&#93; The job's ID.
#'
#' @keywords internal
#'
#' @rdname omics_cancel_annotation_import_job
omics_cancel_annotation_import_job <- function(jobId) {
  op <- new_operation(
    name = "CancelAnnotationImportJob",
    http_method = "DELETE",
    http_path = "/import/annotation/{jobId}",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$cancel_annotation_import_job_input(jobId = jobId)
  output <- .omics$cancel_annotation_import_job_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$cancel_annotation_import_job <- omics_cancel_annotation_import_job

#' Cancels a run using its ID and returns a response with no body if the
#' operation is successful
#'
#' @description
#' 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 [`list_runs`][omics_list_runs] API operation to check that it is no longer listed.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_cancel_run/](https://www.paws-r-sdk.com/docs/omics_cancel_run/) for full documentation.
#'
#' @param id &#91;required&#93; The run's ID.
#'
#' @keywords internal
#'
#' @rdname omics_cancel_run
omics_cancel_run <- function(id) {
  op <- new_operation(
    name = "CancelRun",
    http_method = "POST",
    http_path = "/run/{id}/cancel",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$cancel_run_input(id = id)
  output <- .omics$cancel_run_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$cancel_run <- omics_cancel_run

#' Cancels all runs within a specified batch
#'
#' @description
#' Cancels all runs within a specified batch. This operation prevents not-yet-submitted runs from starting and submits [`cancel_run`][omics_cancel_run] requests for runs that have already started.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_cancel_run_batch/](https://www.paws-r-sdk.com/docs/omics_cancel_run_batch/) for full documentation.
#'
#' @param batchId &#91;required&#93; The identifier portion of the run batch ARN.
#'
#' @keywords internal
#'
#' @rdname omics_cancel_run_batch
omics_cancel_run_batch <- function(batchId) {
  op <- new_operation(
    name = "CancelRunBatch",
    http_method = "POST",
    http_path = "/runBatch/cancel",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$cancel_run_batch_input(batchId = batchId)
  output <- .omics$cancel_run_batch_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$cancel_run_batch <- omics_cancel_run_batch

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_cancel_variant_import_job/](https://www.paws-r-sdk.com/docs/omics_cancel_variant_import_job/) for full documentation.
#'
#' @param jobId &#91;required&#93; The job's ID.
#'
#' @keywords internal
#'
#' @rdname omics_cancel_variant_import_job
omics_cancel_variant_import_job <- function(jobId) {
  op <- new_operation(
    name = "CancelVariantImportJob",
    http_method = "DELETE",
    http_path = "/import/variant/{jobId}",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$cancel_variant_import_job_input(jobId = jobId)
  output <- .omics$cancel_variant_import_job_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$cancel_variant_import_job <- omics_cancel_variant_import_job

#' 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
#'
#' @description
#' Completes a multipart read set upload into a sequence store after you have initiated the upload process with [`create_multipart_read_set_upload`][omics_create_multipart_read_set_upload] and uploaded all read set parts using [`upload_read_set_part`][omics_upload_read_set_part]. 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).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_complete_multipart_read_set_upload/](https://www.paws-r-sdk.com/docs/omics_complete_multipart_read_set_upload/) for full documentation.
#'
#' @param sequenceStoreId &#91;required&#93; The sequence store ID for the store involved in the multipart upload.
#' @param uploadId &#91;required&#93; The ID for the multipart upload.
#' @param parts &#91;required&#93; The individual uploads or parts of a multipart upload.
#'
#' @keywords internal
#'
#' @rdname omics_complete_multipart_read_set_upload
omics_complete_multipart_read_set_upload <- function(sequenceStoreId, uploadId, parts) {
  op <- new_operation(
    name = "CompleteMultipartReadSetUpload",
    http_method = "POST",
    http_path = "/sequencestore/{sequenceStoreId}/upload/{uploadId}/complete",
    host_prefix = "storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$complete_multipart_read_set_upload_input(sequenceStoreId = sequenceStoreId, uploadId = uploadId, parts = parts)
  output <- .omics$complete_multipart_read_set_upload_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$complete_multipart_read_set_upload <- omics_complete_multipart_read_set_upload

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_create_annotation_store/](https://www.paws-r-sdk.com/docs/omics_create_annotation_store/) for full documentation.
#'
#' @param reference The genome reference for the store's annotations.
#' @param name A name for the store.
#' @param description A description for the store.
#' @param tags Tags for the store.
#' @param versionName The name given to an annotation store version to distinguish it from other versions.
#' @param sseConfig Server-side encryption (SSE) settings for the store.
#' @param storeFormat &#91;required&#93; The annotation file format of the store.
#' @param storeOptions File parsing options for the annotation store.
#'
#' @keywords internal
#'
#' @rdname omics_create_annotation_store
omics_create_annotation_store <- function(reference = NULL, name = NULL, description = NULL, tags = NULL, versionName = NULL, sseConfig = NULL, storeFormat, storeOptions = NULL) {
  op <- new_operation(
    name = "CreateAnnotationStore",
    http_method = "POST",
    http_path = "/annotationStore",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$create_annotation_store_input(reference = reference, name = name, description = description, tags = tags, versionName = versionName, sseConfig = sseConfig, storeFormat = storeFormat, storeOptions = storeOptions)
  output <- .omics$create_annotation_store_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$create_annotation_store <- omics_create_annotation_store

#' Creates a new version of an annotation store
#'
#' @description
#' Creates a new version of an annotation store.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_create_annotation_store_version/](https://www.paws-r-sdk.com/docs/omics_create_annotation_store_version/) for full documentation.
#'
#' @param name &#91;required&#93; The name of an annotation store version from which versions are being created.
#' @param versionName &#91;required&#93; The name given to an annotation store version to distinguish it from other versions.
#' @param description The description of an annotation store version.
#' @param versionOptions The options for an annotation store version.
#' @param tags Any tags added to annotation store version.
#'
#' @keywords internal
#'
#' @rdname omics_create_annotation_store_version
omics_create_annotation_store_version <- function(name, versionName, description = NULL, versionOptions = NULL, tags = NULL) {
  op <- new_operation(
    name = "CreateAnnotationStoreVersion",
    http_method = "POST",
    http_path = "/annotationStore/{name}/version",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$create_annotation_store_version_input(name = name, versionName = versionName, description = description, versionOptions = versionOptions, tags = tags)
  output <- .omics$create_annotation_store_version_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$create_annotation_store_version <- omics_create_annotation_store_version

#' Create a new configuration
#'
#' @description
#' Create a new configuration.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_create_configuration/](https://www.paws-r-sdk.com/docs/omics_create_configuration/) for full documentation.
#'
#' @param name &#91;required&#93; User-friendly name for the configuration.
#' @param description Optional description for the configuration.
#' @param runConfigurations &#91;required&#93; Required run-specific configurations.
#' @param tags Optional tags for the configuration.
#' @param requestId &#91;required&#93; Optional request idempotency token. If not specified, a universally unique identifier (UUID) will be automatically generated for the request.
#'
#' @keywords internal
#'
#' @rdname omics_create_configuration
omics_create_configuration <- function(name, description = NULL, runConfigurations, tags = NULL, requestId) {
  op <- new_operation(
    name = "CreateConfiguration",
    http_method = "POST",
    http_path = "/configuration",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$create_configuration_input(name = name, description = description, runConfigurations = runConfigurations, tags = tags, requestId = requestId)
  output <- .omics$create_configuration_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$create_configuration <- omics_create_configuration

#' Initiates a multipart read set upload for uploading partitioned source
#' files into a sequence store
#'
#' @description
#' 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 [`upload_read_set_part`][omics_upload_read_set_part] API operation to upload parts into a sequence store.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_create_multipart_read_set_upload/](https://www.paws-r-sdk.com/docs/omics_create_multipart_read_set_upload/) for full documentation.
#'
#' @param sequenceStoreId &#91;required&#93; The sequence store ID for the store that is the destination of the multipart uploads.
#' @param clientToken An idempotency token that can be used to avoid triggering multiple multipart uploads.
#' @param sourceFileType &#91;required&#93; The type of file being uploaded.
#' @param subjectId &#91;required&#93; The source's subject ID.
#' @param sampleId &#91;required&#93; The source's sample ID.
#' @param generatedFrom Where the source originated.
#' @param referenceArn The ARN of the reference.
#' @param name &#91;required&#93; The name of the read set.
#' @param description The description of the read set.
#' @param tags Any tags to add to the read set.
#'
#' @keywords internal
#'
#' @rdname omics_create_multipart_read_set_upload
omics_create_multipart_read_set_upload <- function(sequenceStoreId, clientToken = NULL, sourceFileType, subjectId, sampleId, generatedFrom = NULL, referenceArn = NULL, name, description = NULL, tags = NULL) {
  op <- new_operation(
    name = "CreateMultipartReadSetUpload",
    http_method = "POST",
    http_path = "/sequencestore/{sequenceStoreId}/upload",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$create_multipart_read_set_upload_input(sequenceStoreId = sequenceStoreId, clientToken = clientToken, sourceFileType = sourceFileType, subjectId = subjectId, sampleId = sampleId, generatedFrom = generatedFrom, referenceArn = referenceArn, name = name, description = description, tags = tags)
  output <- .omics$create_multipart_read_set_upload_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$create_multipart_read_set_upload <- omics_create_multipart_read_set_upload

#' Creates a reference store and returns metadata in JSON format
#'
#' @description
#' 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 [`start_reference_import_job`][omics_start_reference_import_job] API operation.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_create_reference_store/](https://www.paws-r-sdk.com/docs/omics_create_reference_store/) for full documentation.
#'
#' @param name &#91;required&#93; A name for the store.
#' @param description A description for the store.
#' @param sseConfig Server-side encryption (SSE) settings for the store.
#' @param tags Tags for the store.
#' @param clientToken To ensure that requests don't run multiple times, specify a unique token for each request.
#'
#' @keywords internal
#'
#' @rdname omics_create_reference_store
omics_create_reference_store <- function(name, description = NULL, sseConfig = NULL, tags = NULL, clientToken = NULL) {
  op <- new_operation(
    name = "CreateReferenceStore",
    http_method = "POST",
    http_path = "/referencestore",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$create_reference_store_input(name = name, description = description, sseConfig = sseConfig, tags = tags, clientToken = clientToken)
  output <- .omics$create_reference_store_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$create_reference_store <- omics_create_reference_store

#' Creates a run cache to store and reference task outputs from completed
#' private runs
#'
#' @description
#' 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.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_create_run_cache/](https://www.paws-r-sdk.com/docs/omics_create_run_cache/) for full documentation.
#'
#' @param cacheBehavior Default cache behavior for runs that use this cache. Supported values are:
#' 
#' `CACHE_ON_FAILURE`: Caches task outputs from completed tasks for runs that fail. This setting is useful if you're debugging a workflow that fails after several tasks completed successfully. The subsequent run uses the cache outputs for previously-completed tasks if the task definition, inputs, and container in ECR are identical to the prior run.
#' 
#' `CACHE_ALWAYS`: Caches task outputs from completed tasks for all runs. This setting is useful in development mode, but do not use it in a production setting.
#' 
#' If you don't specify a value, the default behavior is CACHE_ON_FAILURE. When you start a run that uses this cache, you can override the default cache behavior.
#' 
#' For more information, see [Run cache behavior](https://docs.aws.amazon.com/omics/latest/dev/how-run-cache.html#run-cache-behavior) in the *Amazon Web Services HealthOmics User Guide*.
#' @param cacheS3Location &#91;required&#93; Specify the S3 location for storing the cached task outputs. This data must be immediately accessible (not in an archived state).
#' @param description Enter a description of the run cache.
#' @param name Enter a user-friendly name for the run cache.
#' @param requestId &#91;required&#93; A unique request token, to ensure idempotency. If you don't specify a token, Amazon Web Services HealthOmics automatically generates a universally unique identifier (UUID) for the request.
#' @param tags Specify one or more tags to associate with this run cache.
#' @param cacheBucketOwnerId The Amazon Web Services account ID of the expected owner of the S3 bucket for the run cache. If not provided, your account ID is set as the owner of the bucket.
#'
#' @keywords internal
#'
#' @rdname omics_create_run_cache
omics_create_run_cache <- function(cacheBehavior = NULL, cacheS3Location, description = NULL, name = NULL, requestId, tags = NULL, cacheBucketOwnerId = NULL) {
  op <- new_operation(
    name = "CreateRunCache",
    http_method = "POST",
    http_path = "/runCache",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$create_run_cache_input(cacheBehavior = cacheBehavior, cacheS3Location = cacheS3Location, description = description, name = name, requestId = requestId, tags = tags, cacheBucketOwnerId = cacheBucketOwnerId)
  output <- .omics$create_run_cache_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$create_run_cache <- omics_create_run_cache

#' Creates a run group to limit the compute resources for the runs that are
#' added to the group
#'
#' @description
#' 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.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_create_run_group/](https://www.paws-r-sdk.com/docs/omics_create_run_group/) for full documentation.
#'
#' @param name A name for the group.
#' @param maxCpus The maximum number of CPUs that can run concurrently across all active runs in the run group.
#' @param maxRuns The maximum number of runs that can be running at the same time.
#' @param maxDuration The maximum time for each run (in minutes). If a run exceeds the maximum run time, the run fails automatically.
#' @param tags Tags for the group.
#' @param requestId &#91;required&#93; To ensure that requests don't run multiple times, specify a unique ID for each request.
#' @param maxGpus The maximum number of GPUs that can run concurrently across all active runs in the run group.
#'
#' @keywords internal
#'
#' @rdname omics_create_run_group
omics_create_run_group <- function(name = NULL, maxCpus = NULL, maxRuns = NULL, maxDuration = NULL, tags = NULL, requestId, maxGpus = NULL) {
  op <- new_operation(
    name = "CreateRunGroup",
    http_method = "POST",
    http_path = "/runGroup",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$create_run_group_input(name = name, maxCpus = maxCpus, maxRuns = maxRuns, maxDuration = maxDuration, tags = tags, requestId = requestId, maxGpus = maxGpus)
  output <- .omics$create_run_group_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$create_run_group <- omics_create_run_group

#' Creates a sequence store and returns its metadata
#'
#' @description
#' 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.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_create_sequence_store/](https://www.paws-r-sdk.com/docs/omics_create_sequence_store/) for full documentation.
#'
#' @param name &#91;required&#93; A name for the store.
#' @param description A description for the store.
#' @param sseConfig Server-side encryption (SSE) settings for the store.
#' @param tags Tags for the store. You can configure up to 50 tags.
#' @param clientToken An idempotency token used to dedupe retry requests so that duplicate runs are not created.
#' @param fallbackLocation An S3 location that is used to store files that have failed a direct upload. You can add or change the `fallbackLocation` after creating a sequence store. This is not required if you are uploading files from a different S3 bucket.
#' @param eTagAlgorithmFamily The ETag algorithm family to use for ingested read sets. The default value is MD5up. For more information on ETags, see [ETags and data provenance](https://docs.aws.amazon.com/omics/latest/dev/etags-and-provenance.html) in the *Amazon Web Services HealthOmics User Guide*.
#' @param propagatedSetLevelTags The tags keys to propagate to the S3 objects associated with read sets in the sequence store. These tags can be used as input to add metadata to your read sets.
#' @param s3AccessConfig S3 access configuration parameters. This specifies the parameters needed to access logs stored in S3 buckets. The S3 bucket must be in the same region and account as the sequence store.
#'
#' @keywords internal
#'
#' @rdname omics_create_sequence_store
omics_create_sequence_store <- function(name, description = NULL, sseConfig = NULL, tags = NULL, clientToken = NULL, fallbackLocation = NULL, eTagAlgorithmFamily = NULL, propagatedSetLevelTags = NULL, s3AccessConfig = NULL) {
  op <- new_operation(
    name = "CreateSequenceStore",
    http_method = "POST",
    http_path = "/sequencestore",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$create_sequence_store_input(name = name, description = description, sseConfig = sseConfig, tags = tags, clientToken = clientToken, fallbackLocation = fallbackLocation, eTagAlgorithmFamily = eTagAlgorithmFamily, propagatedSetLevelTags = propagatedSetLevelTags, s3AccessConfig = s3AccessConfig)
  output <- .omics$create_sequence_store_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$create_sequence_store <- omics_create_sequence_store

#' Creates a cross-account shared resource
#'
#' @description
#' 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).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_create_share/](https://www.paws-r-sdk.com/docs/omics_create_share/) for full documentation.
#'
#' @param resourceArn &#91;required&#93; The ARN of the resource to be shared.
#' @param principalSubscriber &#91;required&#93; The principal subscriber is the account being offered shared access to the resource.
#' @param shareName A name that the owner defines for the share.
#'
#' @keywords internal
#'
#' @rdname omics_create_share
omics_create_share <- function(resourceArn, principalSubscriber, shareName = NULL) {
  op <- new_operation(
    name = "CreateShare",
    http_method = "POST",
    http_path = "/share",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$create_share_input(resourceArn = resourceArn, principalSubscriber = principalSubscriber, shareName = shareName)
  output <- .omics$create_share_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$create_share <- omics_create_share

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_create_variant_store/](https://www.paws-r-sdk.com/docs/omics_create_variant_store/) for full documentation.
#'
#' @param reference &#91;required&#93; The genome reference for the store's variants.
#' @param name A name for the store.
#' @param description A description for the store.
#' @param tags Tags for the store.
#' @param sseConfig Server-side encryption (SSE) settings for the store.
#'
#' @keywords internal
#'
#' @rdname omics_create_variant_store
omics_create_variant_store <- function(reference, name = NULL, description = NULL, tags = NULL, sseConfig = NULL) {
  op <- new_operation(
    name = "CreateVariantStore",
    http_method = "POST",
    http_path = "/variantStore",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$create_variant_store_input(reference = reference, name = name, description = description, tags = tags, sseConfig = sseConfig)
  output <- .omics$create_variant_store_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$create_variant_store <- omics_create_variant_store

#' Creates a private workflow
#'
#' @description
#' Creates a private workflow. Before you create a private workflow, you must create and configure these required resources:
#'
#' See [https://www.paws-r-sdk.com/docs/omics_create_workflow/](https://www.paws-r-sdk.com/docs/omics_create_workflow/) for full documentation.
#'
#' @param name Name (optional but highly recommended) for the workflow to locate relevant information in the CloudWatch logs and Amazon Web Services HealthOmics console.
#' @param description A description for the workflow.
#' @param engine The workflow engine for the workflow. By default, Amazon Web Services HealthOmics detects the engine automatically from your workflow definition. Provide a value if you have workflow definition files from more than one engine in your zip file, or to use WDL lenient.
#' 
#' WDL lenient is designed to handle workflows migrated from Cromwell. It supports customer Cromwell directives and some non-conformant logic. For details, see [Implicit type conversion in WDL lenient](https://docs.aws.amazon.com/omics/latest/dev/) in the *Amazon Web Services HealthOmics User Guide*.
#' @param definitionZip A ZIP archive containing the main workflow definition file and dependencies that it imports for the workflow. You can use a file with a ://fileb prefix instead of the Base64 string. For more information, see [Workflow definition requirements](https://docs.aws.amazon.com/omics/latest/dev/workflow-defn-requirements.html) in the *Amazon Web Services HealthOmics User Guide*.
#' @param definitionUri The S3 URI of a definition for the workflow. The S3 bucket must be in the same region as the workflow.
#' @param main The path of the main definition file for the workflow. This parameter is not required if the ZIP archive contains only one workflow definition file, or if the main definition file is named “main”. An example path is: `workflow-definition/main-file.wdl`.
#' @param parameterTemplate A parameter template for the workflow. If this field is blank, Amazon Web Services HealthOmics will automatically parse the parameter template values from your workflow definition file. To override these service generated default values, provide a parameter template. To view an example of a parameter template, see [Parameter template files](https://docs.aws.amazon.com/omics/latest/dev/parameter-templates.html) in the *Amazon Web Services HealthOmics User Guide*.
#' @param storageCapacity The default static storage capacity (in gibibytes) for runs that use this workflow or workflow version. The `storageCapacity` can be overwritten at run time. The storage capacity is not required for runs with a `DYNAMIC` storage type.
#' @param tags Tags for the workflow. You can define up to 50 tags for the workflow. For more information, see [Adding a tag](https://docs.aws.amazon.com/omics/latest/dev/add-a-tag.html) in the *Amazon Web Services HealthOmics User Guide*.
#' @param requestId &#91;required&#93; An idempotency token to ensure that duplicate workflows are not created when Amazon Web Services HealthOmics submits retry requests.
#' @param accelerators The computational accelerator specified to run the workflow.
#' @param storageType The default storage type for runs that use this workflow. The `storageType` can be overridden at run time. `DYNAMIC` storage dynamically scales the storage up or down, based on file system utilization. `STATIC` storage allocates a fixed amount of storage. For more information about dynamic and static storage types, see [Run storage types](https://docs.aws.amazon.com/omics/latest/dev/workflows-run-types.html) in the *Amazon Web Services HealthOmics User Guide*.
#' @param containerRegistryMap (Optional) Use a container registry map to specify mappings between the ECR private repository and one or more upstream registries. For more information, see [Container images](https://docs.aws.amazon.com/omics/latest/dev/workflows-ecr.html) in the *Amazon Web Services HealthOmics User Guide*.
#' @param containerRegistryMapUri (Optional) URI of the S3 location for the registry mapping file.
#' @param readmeMarkdown The markdown content for the workflow's README file. This provides documentation and usage information for users of the workflow.
#' @param parameterTemplatePath The path to the workflow parameter template JSON file within the repository. This file defines the input parameters for runs that use this workflow. If not specified, the workflow will be created without a parameter template.
#' @param readmePath The path to the workflow README markdown file within the repository. This file provides documentation and usage information for the workflow. If not specified, the `README.md` file from the root directory of the repository will be used.
#' @param definitionRepository The repository information for the workflow definition. This allows you to source your workflow definition directly from a code repository.
#' @param workflowBucketOwnerId The Amazon Web Services account ID of the expected owner of the S3 bucket that contains the workflow definition. If not specified, the service skips the validation.
#' @param readmeUri The S3 URI of the README file for the workflow. This file provides documentation and usage information for the workflow. Requirements include:
#' 
#' -   The S3 URI must begin with `s3://USER-OWNED-BUCKET/`
#' 
#' -   The requester must have access to the S3 bucket and object.
#' 
#' -   The max README content length is 500 KiB.
#'
#' @keywords internal
#'
#' @rdname omics_create_workflow
omics_create_workflow <- function(name = NULL, description = NULL, engine = NULL, definitionZip = NULL, definitionUri = NULL, main = NULL, parameterTemplate = NULL, storageCapacity = NULL, tags = NULL, requestId, accelerators = NULL, storageType = NULL, containerRegistryMap = NULL, containerRegistryMapUri = NULL, readmeMarkdown = NULL, parameterTemplatePath = NULL, readmePath = NULL, definitionRepository = NULL, workflowBucketOwnerId = NULL, readmeUri = NULL) {
  op <- new_operation(
    name = "CreateWorkflow",
    http_method = "POST",
    http_path = "/workflow",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$create_workflow_input(name = name, description = description, engine = engine, definitionZip = definitionZip, definitionUri = definitionUri, main = main, parameterTemplate = parameterTemplate, storageCapacity = storageCapacity, tags = tags, requestId = requestId, accelerators = accelerators, storageType = storageType, containerRegistryMap = containerRegistryMap, containerRegistryMapUri = containerRegistryMapUri, readmeMarkdown = readmeMarkdown, parameterTemplatePath = parameterTemplatePath, readmePath = readmePath, definitionRepository = definitionRepository, workflowBucketOwnerId = workflowBucketOwnerId, readmeUri = readmeUri)
  output <- .omics$create_workflow_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$create_workflow <- omics_create_workflow

#' Creates a new workflow version for the workflow that you specify with
#' the workflowId parameter
#'
#' @description
#' Creates a new workflow version for the workflow that you specify with the `workflowId` parameter.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_create_workflow_version/](https://www.paws-r-sdk.com/docs/omics_create_workflow_version/) for full documentation.
#'
#' @param workflowId &#91;required&#93; The ID of the workflow where you are creating the new version. The `workflowId` is not the UUID.
#' @param versionName &#91;required&#93; A name for the workflow version. Provide a version name that is unique for this workflow. You cannot change the name after HealthOmics creates the version.
#' 
#' The version name must start with a letter or number and it can include upper-case and lower-case letters, numbers, hyphens, periods and underscores. The maximum length is 64 characters. You can use a simple naming scheme, such as version1, version2, version3. You can also match your workflow versions with your own internal versioning conventions, such as 2.7.0, 2.7.1, 2.7.2.
#' @param definitionZip A ZIP archive containing the main workflow definition file and dependencies that it imports for this workflow version. You can use a file with a ://fileb prefix instead of the Base64 string. For more information, see Workflow definition requirements in the *Amazon Web Services HealthOmics User Guide*.
#' @param definitionUri The S3 URI of a definition for this workflow version. The S3 bucket must be in the same region as this workflow version.
#' @param accelerators The computational accelerator for this workflow version.
#' @param description A description for this workflow version.
#' @param engine The workflow engine for this workflow version. This is only required if you have workflow definition files from more than one engine in your zip file. Otherwise, the service can detect the engine automatically from your workflow definition.
#' @param main The path of the main definition file for this workflow version. This parameter is not required if the ZIP archive contains only one workflow definition file, or if the main definition file is named “main”. An example path is: `workflow-definition/main-file.wdl`.
#' @param parameterTemplate A parameter template for this workflow version. If this field is blank, Amazon Web Services HealthOmics will automatically parse the parameter template values from your workflow definition file. To override these service generated default values, provide a parameter template. To view an example of a parameter template, see [Parameter template files](https://docs.aws.amazon.com/omics/latest/dev/parameter-templates.html) in the *Amazon Web Services HealthOmics User Guide*.
#' @param requestId &#91;required&#93; An idempotency token to ensure that duplicate workflows are not created when Amazon Web Services HealthOmics submits retry requests.
#' @param storageType The default storage type for runs that use this workflow version. The `storageType` can be overridden at run time. `DYNAMIC` storage dynamically scales the storage up or down, based on file system utilization. STATIC storage allocates a fixed amount of storage. For more information about dynamic and static storage types, see [Run storage types](https://docs.aws.amazon.com/omics/latest/dev/workflows-run-types.html) in the *Amazon Web Services HealthOmics User Guide*.
#' @param storageCapacity The default static storage capacity (in gibibytes) for runs that use this workflow version. The `storageCapacity` can be overwritten at run time. The storage capacity is not required for runs with a `DYNAMIC` storage type.
#' @param tags Tags for this workflow version. You can define up to 50 tags for the workflow. For more information, see [Adding a tag](https://docs.aws.amazon.com/omics/latest/dev/add-a-tag.html) in the *Amazon Web Services HealthOmics User Guide*.
#' @param workflowBucketOwnerId Amazon Web Services Id of the owner of the S3 bucket that contains the workflow definition. You need to specify this parameter if your account is not the bucket owner.
#' @param containerRegistryMap (Optional) Use a container registry map to specify mappings between the ECR private repository and one or more upstream registries. For more information, see [Container images](https://docs.aws.amazon.com/omics/latest/dev/workflows-ecr.html) in the *Amazon Web Services HealthOmics User Guide*.
#' @param containerRegistryMapUri (Optional) URI of the S3 location for the registry mapping file.
#' @param readmeMarkdown The markdown content for the workflow version's README file. This provides documentation and usage information for users of this specific workflow version.
#' @param parameterTemplatePath The path to the workflow version parameter template JSON file within the repository. This file defines the input parameters for runs that use this workflow version. If not specified, the workflow version will be created without a parameter template.
#' @param readmePath The path to the workflow version README markdown file within the repository. This file provides documentation and usage information for the workflow. If not specified, the `README.md` file from the root directory of the repository will be used.
#' @param definitionRepository The repository information for the workflow version definition. This allows you to source your workflow version definition directly from a code repository.
#' @param readmeUri The S3 URI of the README file for the workflow version. This file provides documentation and usage information for the workflow version. Requirements include:
#' 
#' -   The S3 URI must begin with `s3://USER-OWNED-BUCKET/`
#' 
#' -   The requester must have access to the S3 bucket and object.
#' 
#' -   The max README content length is 500 KiB.
#'
#' @keywords internal
#'
#' @rdname omics_create_workflow_version
omics_create_workflow_version <- function(workflowId, versionName, definitionZip = NULL, definitionUri = NULL, accelerators = NULL, description = NULL, engine = NULL, main = NULL, parameterTemplate = NULL, requestId, storageType = NULL, storageCapacity = NULL, tags = NULL, workflowBucketOwnerId = NULL, containerRegistryMap = NULL, containerRegistryMapUri = NULL, readmeMarkdown = NULL, parameterTemplatePath = NULL, readmePath = NULL, definitionRepository = NULL, readmeUri = NULL) {
  op <- new_operation(
    name = "CreateWorkflowVersion",
    http_method = "POST",
    http_path = "/workflow/{workflowId}/version",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$create_workflow_version_input(workflowId = workflowId, versionName = versionName, definitionZip = definitionZip, definitionUri = definitionUri, accelerators = accelerators, description = description, engine = engine, main = main, parameterTemplate = parameterTemplate, requestId = requestId, storageType = storageType, storageCapacity = storageCapacity, tags = tags, workflowBucketOwnerId = workflowBucketOwnerId, containerRegistryMap = containerRegistryMap, containerRegistryMapUri = containerRegistryMapUri, readmeMarkdown = readmeMarkdown, parameterTemplatePath = parameterTemplatePath, readmePath = readmePath, definitionRepository = definitionRepository, readmeUri = readmeUri)
  output <- .omics$create_workflow_version_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$create_workflow_version <- omics_create_workflow_version

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_delete_annotation_store/](https://www.paws-r-sdk.com/docs/omics_delete_annotation_store/) for full documentation.
#'
#' @param name &#91;required&#93; The store's name.
#' @param force Whether to force deletion.
#'
#' @keywords internal
#'
#' @rdname omics_delete_annotation_store
omics_delete_annotation_store <- function(name, force = NULL) {
  op <- new_operation(
    name = "DeleteAnnotationStore",
    http_method = "DELETE",
    http_path = "/annotationStore/{name}",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$delete_annotation_store_input(name = name, force = force)
  output <- .omics$delete_annotation_store_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$delete_annotation_store <- omics_delete_annotation_store

#' Deletes one or multiple versions of an annotation store
#'
#' @description
#' Deletes one or multiple versions of an annotation store.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_delete_annotation_store_versions/](https://www.paws-r-sdk.com/docs/omics_delete_annotation_store_versions/) for full documentation.
#'
#' @param name &#91;required&#93; The name of the annotation store from which versions are being deleted.
#' @param versions &#91;required&#93; The versions of an annotation store to be deleted.
#' @param force Forces the deletion of an annotation store version when imports are in-progress..
#'
#' @keywords internal
#'
#' @rdname omics_delete_annotation_store_versions
omics_delete_annotation_store_versions <- function(name, versions, force = NULL) {
  op <- new_operation(
    name = "DeleteAnnotationStoreVersions",
    http_method = "POST",
    http_path = "/annotationStore/{name}/versions/delete",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$delete_annotation_store_versions_input(name = name, versions = versions, force = force)
  output <- .omics$delete_annotation_store_versions_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$delete_annotation_store_versions <- omics_delete_annotation_store_versions

#' Deletes a run batch resource and its associated metadata
#'
#' @description
#' Deletes a run batch resource and its associated metadata. This operation does not delete the individual workflow runs. To delete the runs, call [`delete_run_batch`][omics_delete_run_batch] before calling [`delete_batch`][omics_delete_batch].
#'
#' See [https://www.paws-r-sdk.com/docs/omics_delete_batch/](https://www.paws-r-sdk.com/docs/omics_delete_batch/) for full documentation.
#'
#' @param batchId &#91;required&#93; The identifier portion of the run batch ARN.
#'
#' @keywords internal
#'
#' @rdname omics_delete_batch
omics_delete_batch <- function(batchId) {
  op <- new_operation(
    name = "DeleteBatch",
    http_method = "DELETE",
    http_path = "/runBatch/{batchId}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$delete_batch_input(batchId = batchId)
  output <- .omics$delete_batch_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$delete_batch <- omics_delete_batch

#' Delete an existing configuration
#'
#' @description
#' Delete an existing configuration.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_delete_configuration/](https://www.paws-r-sdk.com/docs/omics_delete_configuration/) for full documentation.
#'
#' @param name &#91;required&#93; Configuration name to delete.
#'
#' @keywords internal
#'
#' @rdname omics_delete_configuration
omics_delete_configuration <- function(name) {
  op <- new_operation(
    name = "DeleteConfiguration",
    http_method = "DELETE",
    http_path = "/configuration/{name}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$delete_configuration_input(name = name)
  output <- .omics$delete_configuration_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$delete_configuration <- omics_delete_configuration

#' Deletes a reference genome and returns a response with no body if the
#' operation is successful
#'
#' @description
#' 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 [`delete_reference_store`][omics_delete_reference_store] API operation.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_delete_reference/](https://www.paws-r-sdk.com/docs/omics_delete_reference/) for full documentation.
#'
#' @param id &#91;required&#93; The reference's ID.
#' @param referenceStoreId &#91;required&#93; The reference's store ID.
#'
#' @keywords internal
#'
#' @rdname omics_delete_reference
omics_delete_reference <- function(id, referenceStoreId) {
  op <- new_operation(
    name = "DeleteReference",
    http_method = "DELETE",
    http_path = "/referencestore/{referenceStoreId}/reference/{id}",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$delete_reference_input(id = id, referenceStoreId = referenceStoreId)
  output <- .omics$delete_reference_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$delete_reference <- omics_delete_reference

#' Deletes a reference store and returns a response with no body if the
#' operation is successful
#'
#' @description
#' 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 [`delete_reference`][omics_delete_reference].
#'
#' See [https://www.paws-r-sdk.com/docs/omics_delete_reference_store/](https://www.paws-r-sdk.com/docs/omics_delete_reference_store/) for full documentation.
#'
#' @param id &#91;required&#93; The store's ID.
#'
#' @keywords internal
#'
#' @rdname omics_delete_reference_store
omics_delete_reference_store <- function(id) {
  op <- new_operation(
    name = "DeleteReferenceStore",
    http_method = "DELETE",
    http_path = "/referencestore/{id}",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$delete_reference_store_input(id = id)
  output <- .omics$delete_reference_store_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$delete_reference_store <- omics_delete_reference_store

#' Deletes a run and returns a response with no body if the operation is
#' successful
#'
#' @description
#' 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.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_delete_run/](https://www.paws-r-sdk.com/docs/omics_delete_run/) for full documentation.
#'
#' @param id &#91;required&#93; The run's ID.
#'
#' @keywords internal
#'
#' @rdname omics_delete_run
omics_delete_run <- function(id) {
  op <- new_operation(
    name = "DeleteRun",
    http_method = "DELETE",
    http_path = "/run/{id}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$delete_run_input(id = id)
  output <- .omics$delete_run_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$delete_run <- omics_delete_run

#' Deletes the individual workflow runs within a batch
#'
#' @description
#' Deletes the individual workflow runs within a batch. This operation is separate from [`delete_batch`][omics_delete_batch], which removes the batch metadata.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_delete_run_batch/](https://www.paws-r-sdk.com/docs/omics_delete_run_batch/) for full documentation.
#'
#' @param batchId &#91;required&#93; The identifier portion of the run batch ARN.
#'
#' @keywords internal
#'
#' @rdname omics_delete_run_batch
omics_delete_run_batch <- function(batchId) {
  op <- new_operation(
    name = "DeleteRunBatch",
    http_method = "POST",
    http_path = "/runBatch/delete",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$delete_run_batch_input(batchId = batchId)
  output <- .omics$delete_run_batch_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$delete_run_batch <- omics_delete_run_batch

#' Deletes a run cache and returns a response with no body if the operation
#' is successful
#'
#' @description
#' 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.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_delete_run_cache/](https://www.paws-r-sdk.com/docs/omics_delete_run_cache/) for full documentation.
#'
#' @param id &#91;required&#93; Run cache identifier for the cache you want to delete.
#'
#' @keywords internal
#'
#' @rdname omics_delete_run_cache
omics_delete_run_cache <- function(id) {
  op <- new_operation(
    name = "DeleteRunCache",
    http_method = "DELETE",
    http_path = "/runCache/{id}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$delete_run_cache_input(id = id)
  output <- .omics$delete_run_cache_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$delete_run_cache <- omics_delete_run_cache

#' Deletes a run group and returns a response with no body if the operation
#' is successful
#'
#' @description
#' Deletes a run group and returns a response with no body if the operation is successful.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_delete_run_group/](https://www.paws-r-sdk.com/docs/omics_delete_run_group/) for full documentation.
#'
#' @param id &#91;required&#93; The run group's ID.
#'
#' @keywords internal
#'
#' @rdname omics_delete_run_group
omics_delete_run_group <- function(id) {
  op <- new_operation(
    name = "DeleteRunGroup",
    http_method = "DELETE",
    http_path = "/runGroup/{id}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$delete_run_group_input(id = id)
  output <- .omics$delete_run_group_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$delete_run_group <- omics_delete_run_group

#' Deletes an access policy for the specified store
#'
#' @description
#' Deletes an access policy for the specified store.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_delete_s3_access_policy/](https://www.paws-r-sdk.com/docs/omics_delete_s3_access_policy/) for full documentation.
#'
#' @param s3AccessPointArn &#91;required&#93; The S3 access point ARN that has the access policy.
#'
#' @keywords internal
#'
#' @rdname omics_delete_s3_access_policy
omics_delete_s3_access_policy <- function(s3AccessPointArn) {
  op <- new_operation(
    name = "DeleteS3AccessPolicy",
    http_method = "DELETE",
    http_path = "/s3accesspolicy/{s3AccessPointArn}",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$delete_s3_access_policy_input(s3AccessPointArn = s3AccessPointArn)
  output <- .omics$delete_s3_access_policy_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$delete_s3_access_policy <- omics_delete_s3_access_policy

#' Deletes a sequence store and returns a response with no body if the
#' operation is successful
#'
#' @description
#' 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.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_delete_sequence_store/](https://www.paws-r-sdk.com/docs/omics_delete_sequence_store/) for full documentation.
#'
#' @param id &#91;required&#93; The sequence store's ID.
#'
#' @keywords internal
#'
#' @rdname omics_delete_sequence_store
omics_delete_sequence_store <- function(id) {
  op <- new_operation(
    name = "DeleteSequenceStore",
    http_method = "DELETE",
    http_path = "/sequencestore/{id}",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$delete_sequence_store_input(id = id)
  output <- .omics$delete_sequence_store_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$delete_sequence_store <- omics_delete_sequence_store

#' Deletes a resource share
#'
#' @description
#' 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.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_delete_share/](https://www.paws-r-sdk.com/docs/omics_delete_share/) for full documentation.
#'
#' @param shareId &#91;required&#93; The ID for the resource share to be deleted.
#'
#' @keywords internal
#'
#' @rdname omics_delete_share
omics_delete_share <- function(shareId) {
  op <- new_operation(
    name = "DeleteShare",
    http_method = "DELETE",
    http_path = "/share/{shareId}",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$delete_share_input(shareId = shareId)
  output <- .omics$delete_share_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$delete_share <- omics_delete_share

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_delete_variant_store/](https://www.paws-r-sdk.com/docs/omics_delete_variant_store/) for full documentation.
#'
#' @param name &#91;required&#93; The store's name.
#' @param force Whether to force deletion.
#'
#' @keywords internal
#'
#' @rdname omics_delete_variant_store
omics_delete_variant_store <- function(name, force = NULL) {
  op <- new_operation(
    name = "DeleteVariantStore",
    http_method = "DELETE",
    http_path = "/variantStore/{name}",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$delete_variant_store_input(name = name, force = force)
  output <- .omics$delete_variant_store_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$delete_variant_store <- omics_delete_variant_store

#' Deletes a workflow by specifying its ID
#'
#' @description
#' Deletes a workflow by specifying its ID. This operation returns a response with no body if the deletion is successful.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_delete_workflow/](https://www.paws-r-sdk.com/docs/omics_delete_workflow/) for full documentation.
#'
#' @param id &#91;required&#93; The workflow's ID.
#'
#' @keywords internal
#'
#' @rdname omics_delete_workflow
omics_delete_workflow <- function(id) {
  op <- new_operation(
    name = "DeleteWorkflow",
    http_method = "DELETE",
    http_path = "/workflow/{id}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$delete_workflow_input(id = id)
  output <- .omics$delete_workflow_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$delete_workflow <- omics_delete_workflow

#' Deletes a workflow version
#'
#' @description
#' Deletes a workflow version. Deleting a workflow version doesn't affect any ongoing runs that are using the workflow version.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_delete_workflow_version/](https://www.paws-r-sdk.com/docs/omics_delete_workflow_version/) for full documentation.
#'
#' @param workflowId &#91;required&#93; The workflow's ID.
#' @param versionName &#91;required&#93; The workflow version name.
#'
#' @keywords internal
#'
#' @rdname omics_delete_workflow_version
omics_delete_workflow_version <- function(workflowId, versionName) {
  op <- new_operation(
    name = "DeleteWorkflowVersion",
    http_method = "DELETE",
    http_path = "/workflow/{workflowId}/version/{versionName}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$delete_workflow_version_input(workflowId = workflowId, versionName = versionName)
  output <- .omics$delete_workflow_version_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$delete_workflow_version <- omics_delete_workflow_version

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_annotation_import_job/](https://www.paws-r-sdk.com/docs/omics_get_annotation_import_job/) for full documentation.
#'
#' @param jobId &#91;required&#93; The job's ID.
#'
#' @keywords internal
#'
#' @rdname omics_get_annotation_import_job
omics_get_annotation_import_job <- function(jobId) {
  op <- new_operation(
    name = "GetAnnotationImportJob",
    http_method = "GET",
    http_path = "/import/annotation/{jobId}",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_annotation_import_job_input(jobId = jobId)
  output <- .omics$get_annotation_import_job_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_annotation_import_job <- omics_get_annotation_import_job

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_annotation_store/](https://www.paws-r-sdk.com/docs/omics_get_annotation_store/) for full documentation.
#'
#' @param name &#91;required&#93; The store's name.
#'
#' @keywords internal
#'
#' @rdname omics_get_annotation_store
omics_get_annotation_store <- function(name) {
  op <- new_operation(
    name = "GetAnnotationStore",
    http_method = "GET",
    http_path = "/annotationStore/{name}",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_annotation_store_input(name = name)
  output <- .omics$get_annotation_store_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_annotation_store <- omics_get_annotation_store

#' Retrieves the metadata for an annotation store version
#'
#' @description
#' Retrieves the metadata for an annotation store version.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_annotation_store_version/](https://www.paws-r-sdk.com/docs/omics_get_annotation_store_version/) for full documentation.
#'
#' @param name &#91;required&#93; The name given to an annotation store version to distinguish it from others.
#' @param versionName &#91;required&#93; The name given to an annotation store version to distinguish it from others.
#'
#' @keywords internal
#'
#' @rdname omics_get_annotation_store_version
omics_get_annotation_store_version <- function(name, versionName) {
  op <- new_operation(
    name = "GetAnnotationStoreVersion",
    http_method = "GET",
    http_path = "/annotationStore/{name}/version/{versionName}",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_annotation_store_version_input(name = name, versionName = versionName)
  output <- .omics$get_annotation_store_version_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_annotation_store_version <- omics_get_annotation_store_version

#' Retrieves details and current status for a specific run batch, including
#' submission progress and run execution counts
#'
#' @description
#' Retrieves details and current status for a specific run batch, including submission progress and run execution counts.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_batch/](https://www.paws-r-sdk.com/docs/omics_get_batch/) for full documentation.
#'
#' @param batchId &#91;required&#93; The identifier portion of the run batch ARN.
#'
#' @keywords internal
#'
#' @rdname omics_get_batch
omics_get_batch <- function(batchId) {
  op <- new_operation(
    name = "GetBatch",
    http_method = "GET",
    http_path = "/runBatch/{batchId}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_batch_input(batchId = batchId)
  output <- .omics$get_batch_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_batch <- omics_get_batch

#' Retrieve configuration details for specified name
#'
#' @description
#' Retrieve configuration details for specified name.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_configuration/](https://www.paws-r-sdk.com/docs/omics_get_configuration/) for full documentation.
#'
#' @param name &#91;required&#93; Configuration name to retrieve.
#'
#' @keywords internal
#'
#' @rdname omics_get_configuration
omics_get_configuration <- function(name) {
  op <- new_operation(
    name = "GetConfiguration",
    http_method = "GET",
    http_path = "/configuration/{name}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_configuration_input(name = name)
  output <- .omics$get_configuration_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_configuration <- omics_get_configuration

#' Retrieves detailed information from parts of a read set and returns the
#' read set in the same format that it was uploaded
#'
#' @description
#' 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.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_read_set/](https://www.paws-r-sdk.com/docs/omics_get_read_set/) for full documentation.
#'
#' @param id &#91;required&#93; The read set's ID.
#' @param sequenceStoreId &#91;required&#93; The read set's sequence store ID.
#' @param file The file to retrieve.
#' @param partNumber &#91;required&#93; The part number to retrieve.
#'
#' @keywords internal
#'
#' @rdname omics_get_read_set
omics_get_read_set <- function(id, sequenceStoreId, file = NULL, partNumber) {
  op <- new_operation(
    name = "GetReadSet",
    http_method = "GET",
    http_path = "/sequencestore/{sequenceStoreId}/readset/{id}",
    host_prefix = "storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_read_set_input(id = id, sequenceStoreId = sequenceStoreId, file = file, partNumber = partNumber)
  output <- .omics$get_read_set_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_read_set <- omics_get_read_set

#' Returns detailed information about the status of a read set activation
#' job in JSON format
#'
#' @description
#' Returns detailed information about the status of a read set activation job in JSON format.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_read_set_activation_job/](https://www.paws-r-sdk.com/docs/omics_get_read_set_activation_job/) for full documentation.
#'
#' @param id &#91;required&#93; The job's ID.
#' @param sequenceStoreId &#91;required&#93; The job's sequence store ID.
#'
#' @keywords internal
#'
#' @rdname omics_get_read_set_activation_job
omics_get_read_set_activation_job <- function(id, sequenceStoreId) {
  op <- new_operation(
    name = "GetReadSetActivationJob",
    http_method = "GET",
    http_path = "/sequencestore/{sequenceStoreId}/activationjob/{id}",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_read_set_activation_job_input(id = id, sequenceStoreId = sequenceStoreId)
  output <- .omics$get_read_set_activation_job_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_read_set_activation_job <- omics_get_read_set_activation_job

#' Retrieves status information about a read set export job and returns the
#' data in JSON format
#'
#' @description
#' 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.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_read_set_export_job/](https://www.paws-r-sdk.com/docs/omics_get_read_set_export_job/) for full documentation.
#'
#' @param sequenceStoreId &#91;required&#93; The job's sequence store ID.
#' @param id &#91;required&#93; The job's ID.
#'
#' @keywords internal
#'
#' @rdname omics_get_read_set_export_job
omics_get_read_set_export_job <- function(sequenceStoreId, id) {
  op <- new_operation(
    name = "GetReadSetExportJob",
    http_method = "GET",
    http_path = "/sequencestore/{sequenceStoreId}/exportjob/{id}",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_read_set_export_job_input(sequenceStoreId = sequenceStoreId, id = id)
  output <- .omics$get_read_set_export_job_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_read_set_export_job <- omics_get_read_set_export_job

#' Gets detailed and status information about a read set import job and
#' returns the data in JSON format
#'
#' @description
#' Gets detailed and status information about a read set import job and returns the data in JSON format.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_read_set_import_job/](https://www.paws-r-sdk.com/docs/omics_get_read_set_import_job/) for full documentation.
#'
#' @param id &#91;required&#93; The job's ID.
#' @param sequenceStoreId &#91;required&#93; The job's sequence store ID.
#'
#' @keywords internal
#'
#' @rdname omics_get_read_set_import_job
omics_get_read_set_import_job <- function(id, sequenceStoreId) {
  op <- new_operation(
    name = "GetReadSetImportJob",
    http_method = "GET",
    http_path = "/sequencestore/{sequenceStoreId}/importjob/{id}",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_read_set_import_job_input(id = id, sequenceStoreId = sequenceStoreId)
  output <- .omics$get_read_set_import_job_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_read_set_import_job <- omics_get_read_set_import_job

#' Retrieves the metadata for a read set from a sequence store in JSON
#' format
#'
#' @description
#' 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 [`list_tags_for_resource`][omics_list_tags_for_resource] API operation.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_read_set_metadata/](https://www.paws-r-sdk.com/docs/omics_get_read_set_metadata/) for full documentation.
#'
#' @param id &#91;required&#93; The read set's ID.
#' @param sequenceStoreId &#91;required&#93; The read set's sequence store ID.
#'
#' @keywords internal
#'
#' @rdname omics_get_read_set_metadata
omics_get_read_set_metadata <- function(id, sequenceStoreId) {
  op <- new_operation(
    name = "GetReadSetMetadata",
    http_method = "GET",
    http_path = "/sequencestore/{sequenceStoreId}/readset/{id}/metadata",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_read_set_metadata_input(id = id, sequenceStoreId = sequenceStoreId)
  output <- .omics$get_read_set_metadata_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_read_set_metadata <- omics_get_read_set_metadata

#' Downloads parts of data from a reference genome and returns the
#' reference file in the same format that it was uploaded
#'
#' @description
#' Downloads parts of data from a reference genome and returns the reference file in the same format that it was uploaded.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_reference/](https://www.paws-r-sdk.com/docs/omics_get_reference/) for full documentation.
#'
#' @param id &#91;required&#93; The reference's ID.
#' @param referenceStoreId &#91;required&#93; The reference's store ID.
#' @param range The range to retrieve.
#' @param partNumber &#91;required&#93; The part number to retrieve.
#' @param file The file to retrieve.
#'
#' @keywords internal
#'
#' @rdname omics_get_reference
omics_get_reference <- function(id, referenceStoreId, range = NULL, partNumber, file = NULL) {
  op <- new_operation(
    name = "GetReference",
    http_method = "GET",
    http_path = "/referencestore/{referenceStoreId}/reference/{id}",
    host_prefix = "storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_reference_input(id = id, referenceStoreId = referenceStoreId, range = range, partNumber = partNumber, file = file)
  output <- .omics$get_reference_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_reference <- omics_get_reference

#' Monitors the status of a reference import job
#'
#' @description
#' Monitors the status of a reference import job. This operation can be called after calling the [`start_reference_import_job`][omics_start_reference_import_job] operation.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_reference_import_job/](https://www.paws-r-sdk.com/docs/omics_get_reference_import_job/) for full documentation.
#'
#' @param id &#91;required&#93; The job's ID.
#' @param referenceStoreId &#91;required&#93; The job's reference store ID.
#'
#' @keywords internal
#'
#' @rdname omics_get_reference_import_job
omics_get_reference_import_job <- function(id, referenceStoreId) {
  op <- new_operation(
    name = "GetReferenceImportJob",
    http_method = "GET",
    http_path = "/referencestore/{referenceStoreId}/importjob/{id}",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_reference_import_job_input(id = id, referenceStoreId = referenceStoreId)
  output <- .omics$get_reference_import_job_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_reference_import_job <- omics_get_reference_import_job

#' Retrieves metadata for a reference genome
#'
#' @description
#' 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 [`list_tags_for_resource`][omics_list_tags_for_resource] API operation.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_reference_metadata/](https://www.paws-r-sdk.com/docs/omics_get_reference_metadata/) for full documentation.
#'
#' @param id &#91;required&#93; The reference's ID.
#' @param referenceStoreId &#91;required&#93; The reference's reference store ID.
#'
#' @keywords internal
#'
#' @rdname omics_get_reference_metadata
omics_get_reference_metadata <- function(id, referenceStoreId) {
  op <- new_operation(
    name = "GetReferenceMetadata",
    http_method = "GET",
    http_path = "/referencestore/{referenceStoreId}/reference/{id}/metadata",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_reference_metadata_input(id = id, referenceStoreId = referenceStoreId)
  output <- .omics$get_reference_metadata_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_reference_metadata <- omics_get_reference_metadata

#' Gets information about a reference store
#'
#' @description
#' Gets information about a reference store.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_reference_store/](https://www.paws-r-sdk.com/docs/omics_get_reference_store/) for full documentation.
#'
#' @param id &#91;required&#93; The store's ID.
#'
#' @keywords internal
#'
#' @rdname omics_get_reference_store
omics_get_reference_store <- function(id) {
  op <- new_operation(
    name = "GetReferenceStore",
    http_method = "GET",
    http_path = "/referencestore/{id}",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_reference_store_input(id = id)
  output <- .omics$get_reference_store_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_reference_store <- omics_get_reference_store

#' Gets detailed information about a specific run using its ID
#'
#' @description
#' Gets detailed information about a specific run using its ID.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_run/](https://www.paws-r-sdk.com/docs/omics_get_run/) for full documentation.
#'
#' @param id &#91;required&#93; The run's ID.
#' @param export The run's export format.
#'
#' @keywords internal
#'
#' @rdname omics_get_run
omics_get_run <- function(id, export = NULL) {
  op <- new_operation(
    name = "GetRun",
    http_method = "GET",
    http_path = "/run/{id}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_run_input(id = id, export = export)
  output <- .omics$get_run_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_run <- omics_get_run

#' Retrieves detailed information about the specified run cache using its
#' ID
#'
#' @description
#' Retrieves detailed information about the specified run cache using its ID.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_run_cache/](https://www.paws-r-sdk.com/docs/omics_get_run_cache/) for full documentation.
#'
#' @param id &#91;required&#93; The identifier of the run cache to retrieve.
#'
#' @keywords internal
#'
#' @rdname omics_get_run_cache
omics_get_run_cache <- function(id) {
  op <- new_operation(
    name = "GetRunCache",
    http_method = "GET",
    http_path = "/runCache/{id}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_run_cache_input(id = id)
  output <- .omics$get_run_cache_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_run_cache <- omics_get_run_cache

#' Gets information about a run group and returns its metadata
#'
#' @description
#' Gets information about a run group and returns its metadata.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_run_group/](https://www.paws-r-sdk.com/docs/omics_get_run_group/) for full documentation.
#'
#' @param id &#91;required&#93; The group's ID.
#'
#' @keywords internal
#'
#' @rdname omics_get_run_group
omics_get_run_group <- function(id) {
  op <- new_operation(
    name = "GetRunGroup",
    http_method = "GET",
    http_path = "/runGroup/{id}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_run_group_input(id = id)
  output <- .omics$get_run_group_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_run_group <- omics_get_run_group

#' Gets detailed information about a run task using its ID
#'
#' @description
#' Gets detailed information about a run task using its ID.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_run_task/](https://www.paws-r-sdk.com/docs/omics_get_run_task/) for full documentation.
#'
#' @param id &#91;required&#93; The workflow run ID.
#' @param taskId &#91;required&#93; The task's ID.
#'
#' @keywords internal
#'
#' @rdname omics_get_run_task
omics_get_run_task <- function(id, taskId) {
  op <- new_operation(
    name = "GetRunTask",
    http_method = "GET",
    http_path = "/run/{id}/task/{taskId}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_run_task_input(id = id, taskId = taskId)
  output <- .omics$get_run_task_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_run_task <- omics_get_run_task

#' Retrieves details about an access policy on a given store
#'
#' @description
#' Retrieves details about an access policy on a given store.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_s3_access_policy/](https://www.paws-r-sdk.com/docs/omics_get_s3_access_policy/) for full documentation.
#'
#' @param s3AccessPointArn &#91;required&#93; The S3 access point ARN that has the access policy.
#'
#' @keywords internal
#'
#' @rdname omics_get_s3_access_policy
omics_get_s3_access_policy <- function(s3AccessPointArn) {
  op <- new_operation(
    name = "GetS3AccessPolicy",
    http_method = "GET",
    http_path = "/s3accesspolicy/{s3AccessPointArn}",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_s3_access_policy_input(s3AccessPointArn = s3AccessPointArn)
  output <- .omics$get_s3_access_policy_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_s3_access_policy <- omics_get_s3_access_policy

#' Retrieves metadata for a sequence store using its ID and returns it in
#' JSON format
#'
#' @description
#' Retrieves metadata for a sequence store using its ID and returns it in JSON format.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_sequence_store/](https://www.paws-r-sdk.com/docs/omics_get_sequence_store/) for full documentation.
#'
#' @param id &#91;required&#93; The store's ID.
#'
#' @keywords internal
#'
#' @rdname omics_get_sequence_store
omics_get_sequence_store <- function(id) {
  op <- new_operation(
    name = "GetSequenceStore",
    http_method = "GET",
    http_path = "/sequencestore/{id}",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_sequence_store_input(id = id)
  output <- .omics$get_sequence_store_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_sequence_store <- omics_get_sequence_store

#' Retrieves the metadata for the specified resource share
#'
#' @description
#' Retrieves the metadata for the specified resource share.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_share/](https://www.paws-r-sdk.com/docs/omics_get_share/) for full documentation.
#'
#' @param shareId &#91;required&#93; The ID of the share.
#'
#' @keywords internal
#'
#' @rdname omics_get_share
omics_get_share <- function(shareId) {
  op <- new_operation(
    name = "GetShare",
    http_method = "GET",
    http_path = "/share/{shareId}",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_share_input(shareId = shareId)
  output <- .omics$get_share_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_share <- omics_get_share

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_variant_import_job/](https://www.paws-r-sdk.com/docs/omics_get_variant_import_job/) for full documentation.
#'
#' @param jobId &#91;required&#93; The job's ID.
#'
#' @keywords internal
#'
#' @rdname omics_get_variant_import_job
omics_get_variant_import_job <- function(jobId) {
  op <- new_operation(
    name = "GetVariantImportJob",
    http_method = "GET",
    http_path = "/import/variant/{jobId}",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_variant_import_job_input(jobId = jobId)
  output <- .omics$get_variant_import_job_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_variant_import_job <- omics_get_variant_import_job

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_variant_store/](https://www.paws-r-sdk.com/docs/omics_get_variant_store/) for full documentation.
#'
#' @param name &#91;required&#93; The store's name.
#'
#' @keywords internal
#'
#' @rdname omics_get_variant_store
omics_get_variant_store <- function(name) {
  op <- new_operation(
    name = "GetVariantStore",
    http_method = "GET",
    http_path = "/variantStore/{name}",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_variant_store_input(name = name)
  output <- .omics$get_variant_store_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_variant_store <- omics_get_variant_store

#' Gets all information about a workflow using its ID
#'
#' @description
#' Gets all information about a workflow using its ID.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_workflow/](https://www.paws-r-sdk.com/docs/omics_get_workflow/) for full documentation.
#'
#' @param id &#91;required&#93; The workflow's ID.
#' @param type The workflow's type.
#' @param export The export format for the workflow.
#' @param workflowOwnerId The ID of the workflow owner.
#'
#' @keywords internal
#'
#' @rdname omics_get_workflow
omics_get_workflow <- function(id, type = NULL, export = NULL, workflowOwnerId = NULL) {
  op <- new_operation(
    name = "GetWorkflow",
    http_method = "GET",
    http_path = "/workflow/{id}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_workflow_input(id = id, type = type, export = export, workflowOwnerId = workflowOwnerId)
  output <- .omics$get_workflow_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_workflow <- omics_get_workflow

#' Gets information about a workflow version
#'
#' @description
#' Gets information about a workflow version. For more information, see [Workflow versioning in Amazon Web Services HealthOmics](https://docs.aws.amazon.com/omics/latest/dev/workflow-versions.html) in the *Amazon Web Services HealthOmics User Guide*.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_get_workflow_version/](https://www.paws-r-sdk.com/docs/omics_get_workflow_version/) for full documentation.
#'
#' @param workflowId &#91;required&#93; The workflow's ID. The `workflowId` is not the UUID.
#' @param versionName &#91;required&#93; The workflow version name.
#' @param type The workflow's type.
#' @param export The export format for the workflow.
#' @param workflowOwnerId The 12-digit account ID of the workflow owner. The workflow owner ID can be retrieved using the [`get_share`][omics_get_share] API operation. If you are the workflow owner, you do not need to include this ID.
#'
#' @keywords internal
#'
#' @rdname omics_get_workflow_version
omics_get_workflow_version <- function(workflowId, versionName, type = NULL, export = NULL, workflowOwnerId = NULL) {
  op <- new_operation(
    name = "GetWorkflowVersion",
    http_method = "GET",
    http_path = "/workflow/{workflowId}/version/{versionName}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$get_workflow_version_input(workflowId = workflowId, versionName = versionName, type = type, export = export, workflowOwnerId = workflowOwnerId)
  output <- .omics$get_workflow_version_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$get_workflow_version <- omics_get_workflow_version

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_annotation_import_jobs/](https://www.paws-r-sdk.com/docs/omics_list_annotation_import_jobs/) for full documentation.
#'
#' @param maxResults The maximum number of jobs to return in one page of results.
#' @param ids IDs of annotation import jobs to retrieve.
#' @param nextToken Specifies the pagination token from a previous request to retrieve the next page of results.
#' @param filter A filter to apply to the list.
#'
#' @keywords internal
#'
#' @rdname omics_list_annotation_import_jobs
omics_list_annotation_import_jobs <- function(maxResults = NULL, ids = NULL, nextToken = NULL, filter = NULL) {
  op <- new_operation(
    name = "ListAnnotationImportJobs",
    http_method = "POST",
    http_path = "/import/annotations",
    host_prefix = "analytics-",
    paginator = list(input_token = "nextToken", output_token = "nextToken", limit_key = "maxResults", result_key = "annotationImportJobs"),
    stream_api = FALSE
  )
  input <- .omics$list_annotation_import_jobs_input(maxResults = maxResults, ids = ids, nextToken = nextToken, filter = filter)
  output <- .omics$list_annotation_import_jobs_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_annotation_import_jobs <- omics_list_annotation_import_jobs

#' Lists the versions of an annotation store
#'
#' @description
#' Lists the versions of an annotation store.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_annotation_store_versions/](https://www.paws-r-sdk.com/docs/omics_list_annotation_store_versions/) for full documentation.
#'
#' @param name &#91;required&#93; The name of an annotation store.
#' @param maxResults The maximum number of annotation store versions to return in one page of results.
#' @param nextToken Specifies the pagination token from a previous request to retrieve the next page of results.
#' @param filter A filter to apply to the list of annotation store versions.
#'
#' @keywords internal
#'
#' @rdname omics_list_annotation_store_versions
omics_list_annotation_store_versions <- function(name, maxResults = NULL, nextToken = NULL, filter = NULL) {
  op <- new_operation(
    name = "ListAnnotationStoreVersions",
    http_method = "POST",
    http_path = "/annotationStore/{name}/versions",
    host_prefix = "analytics-",
    paginator = list(input_token = "nextToken", output_token = "nextToken", limit_key = "maxResults", result_key = "annotationStoreVersions"),
    stream_api = FALSE
  )
  input <- .omics$list_annotation_store_versions_input(name = name, maxResults = maxResults, nextToken = nextToken, filter = filter)
  output <- .omics$list_annotation_store_versions_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_annotation_store_versions <- omics_list_annotation_store_versions

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_annotation_stores/](https://www.paws-r-sdk.com/docs/omics_list_annotation_stores/) for full documentation.
#'
#' @param ids IDs of stores to list.
#' @param maxResults The maximum number of stores to return in one page of results.
#' @param nextToken Specify the pagination token from a previous request to retrieve the next page of results.
#' @param filter A filter to apply to the list.
#'
#' @keywords internal
#'
#' @rdname omics_list_annotation_stores
omics_list_annotation_stores <- function(ids = NULL, maxResults = NULL, nextToken = NULL, filter = NULL) {
  op <- new_operation(
    name = "ListAnnotationStores",
    http_method = "POST",
    http_path = "/annotationStores",
    host_prefix = "analytics-",
    paginator = list(input_token = "nextToken", output_token = "nextToken", limit_key = "maxResults", result_key = "annotationStores"),
    stream_api = FALSE
  )
  input <- .omics$list_annotation_stores_input(ids = ids, maxResults = maxResults, nextToken = nextToken, filter = filter)
  output <- .omics$list_annotation_stores_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_annotation_stores <- omics_list_annotation_stores

#' Returns a list of run batches in your account, with optional filtering
#' by status, name, or run group
#'
#' @description
#' Returns a list of run batches in your account, with optional filtering by status, name, or run group. Results are paginated. Only one filter per call is supported.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_batch/](https://www.paws-r-sdk.com/docs/omics_list_batch/) for full documentation.
#'
#' @param maxItems The maximum number of batches to return. If not specified, defaults to 100.
#' @param startingToken A pagination token returned from a prior [`list_batch`][omics_list_batch] call.
#' @param status Filter batches by status.
#' @param name Filter batches by name.
#' @param runGroupId Filter batches by run group ID.
#'
#' @keywords internal
#'
#' @rdname omics_list_batch
omics_list_batch <- function(maxItems = NULL, startingToken = NULL, status = NULL, name = NULL, runGroupId = NULL) {
  op <- new_operation(
    name = "ListBatch",
    http_method = "GET",
    http_path = "/runBatch",
    host_prefix = "workflows-",
    paginator = list(input_token = "startingToken", output_token = "nextToken", limit_key = "maxItems", result_key = "items"),
    stream_api = FALSE
  )
  input <- .omics$list_batch_input(maxItems = maxItems, startingToken = startingToken, status = status, name = name, runGroupId = runGroupId)
  output <- .omics$list_batch_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_batch <- omics_list_batch

#' List all configurations for the account
#'
#' @description
#' List all configurations for the account.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_configurations/](https://www.paws-r-sdk.com/docs/omics_list_configurations/) for full documentation.
#'
#' @param maxResults Maximum number of results to return.
#' @param startingToken Pagination token for retrieving next page of results.
#'
#' @keywords internal
#'
#' @rdname omics_list_configurations
omics_list_configurations <- function(maxResults = NULL, startingToken = NULL) {
  op <- new_operation(
    name = "ListConfigurations",
    http_method = "GET",
    http_path = "/configuration",
    host_prefix = "workflows-",
    paginator = list(input_token = "startingToken", output_token = "nextToken", limit_key = "maxResults", result_key = "items"),
    stream_api = FALSE
  )
  input <- .omics$list_configurations_input(maxResults = maxResults, startingToken = startingToken)
  output <- .omics$list_configurations_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_configurations <- omics_list_configurations

#' Lists in-progress multipart read set uploads for a sequence store and
#' returns it in a JSON formatted output
#'
#' @description
#' Lists in-progress multipart read set uploads for a sequence store and returns it in a JSON formatted output. Multipart read set uploads are initiated by the `CreateMultipartReadSetUploads` API operation. This operation returns a response with no body when the upload is complete.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_multipart_read_set_uploads/](https://www.paws-r-sdk.com/docs/omics_list_multipart_read_set_uploads/) for full documentation.
#'
#' @param sequenceStoreId &#91;required&#93; The Sequence Store ID used for the multipart uploads.
#' @param maxResults The maximum number of multipart uploads returned in a page.
#' @param nextToken Next token returned in the response of a previous ListMultipartReadSetUploads call. Used to get the next page of results.
#'
#' @keywords internal
#'
#' @rdname omics_list_multipart_read_set_uploads
omics_list_multipart_read_set_uploads <- function(sequenceStoreId, maxResults = NULL, nextToken = NULL) {
  op <- new_operation(
    name = "ListMultipartReadSetUploads",
    http_method = "POST",
    http_path = "/sequencestore/{sequenceStoreId}/uploads",
    host_prefix = "control-storage-",
    paginator = list(input_token = "nextToken", output_token = "nextToken", limit_key = "maxResults", result_key = "uploads"),
    stream_api = FALSE
  )
  input <- .omics$list_multipart_read_set_uploads_input(sequenceStoreId = sequenceStoreId, maxResults = maxResults, nextToken = nextToken)
  output <- .omics$list_multipart_read_set_uploads_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_multipart_read_set_uploads <- omics_list_multipart_read_set_uploads

#' Retrieves a list of read set activation jobs and returns the metadata in
#' a JSON formatted output
#'
#' @description
#' Retrieves a list of read set activation jobs and returns the metadata in a JSON formatted output. To extract metadata from a read set activation job, use the [`get_read_set_activation_job`][omics_get_read_set_activation_job] API operation.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_read_set_activation_jobs/](https://www.paws-r-sdk.com/docs/omics_list_read_set_activation_jobs/) for full documentation.
#'
#' @param sequenceStoreId &#91;required&#93; The read set's sequence store ID.
#' @param maxResults The maximum number of read set activation jobs to return in one page of results.
#' @param nextToken Specify the pagination token from a previous request to retrieve the next page of results.
#' @param filter A filter to apply to the list.
#'
#' @keywords internal
#'
#' @rdname omics_list_read_set_activation_jobs
omics_list_read_set_activation_jobs <- function(sequenceStoreId, maxResults = NULL, nextToken = NULL, filter = NULL) {
  op <- new_operation(
    name = "ListReadSetActivationJobs",
    http_method = "POST",
    http_path = "/sequencestore/{sequenceStoreId}/activationjobs",
    host_prefix = "control-storage-",
    paginator = list(input_token = "nextToken", output_token = "nextToken", limit_key = "maxResults", result_key = "activationJobs"),
    stream_api = FALSE
  )
  input <- .omics$list_read_set_activation_jobs_input(sequenceStoreId = sequenceStoreId, maxResults = maxResults, nextToken = nextToken, filter = filter)
  output <- .omics$list_read_set_activation_jobs_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_read_set_activation_jobs <- omics_list_read_set_activation_jobs

#' Retrieves a list of read set export jobs in a JSON formatted response
#'
#' @description
#' Retrieves a list of read set export jobs in a JSON formatted response. This API operation is used to check the status of a read set export job initiated by the [`start_read_set_export_job`][omics_start_read_set_export_job] API operation.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_read_set_export_jobs/](https://www.paws-r-sdk.com/docs/omics_list_read_set_export_jobs/) for full documentation.
#'
#' @param sequenceStoreId &#91;required&#93; The jobs' sequence store ID.
#' @param maxResults The maximum number of jobs to return in one page of results.
#' @param nextToken Specify the pagination token from a previous request to retrieve the next page of results.
#' @param filter A filter to apply to the list.
#'
#' @keywords internal
#'
#' @rdname omics_list_read_set_export_jobs
omics_list_read_set_export_jobs <- function(sequenceStoreId, maxResults = NULL, nextToken = NULL, filter = NULL) {
  op <- new_operation(
    name = "ListReadSetExportJobs",
    http_method = "POST",
    http_path = "/sequencestore/{sequenceStoreId}/exportjobs",
    host_prefix = "control-storage-",
    paginator = list(input_token = "nextToken", output_token = "nextToken", limit_key = "maxResults", result_key = "exportJobs"),
    stream_api = FALSE
  )
  input <- .omics$list_read_set_export_jobs_input(sequenceStoreId = sequenceStoreId, maxResults = maxResults, nextToken = nextToken, filter = filter)
  output <- .omics$list_read_set_export_jobs_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_read_set_export_jobs <- omics_list_read_set_export_jobs

#' Retrieves a list of read set import jobs and returns the data in JSON
#' format
#'
#' @description
#' Retrieves a list of read set import jobs and returns the data in JSON format.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_read_set_import_jobs/](https://www.paws-r-sdk.com/docs/omics_list_read_set_import_jobs/) for full documentation.
#'
#' @param maxResults The maximum number of jobs to return in one page of results.
#' @param nextToken Specify the pagination token from a previous request to retrieve the next page of results.
#' @param sequenceStoreId &#91;required&#93; The jobs' sequence store ID.
#' @param filter A filter to apply to the list.
#'
#' @keywords internal
#'
#' @rdname omics_list_read_set_import_jobs
omics_list_read_set_import_jobs <- function(maxResults = NULL, nextToken = NULL, sequenceStoreId, filter = NULL) {
  op <- new_operation(
    name = "ListReadSetImportJobs",
    http_method = "POST",
    http_path = "/sequencestore/{sequenceStoreId}/importjobs",
    host_prefix = "control-storage-",
    paginator = list(input_token = "nextToken", output_token = "nextToken", limit_key = "maxResults", result_key = "importJobs"),
    stream_api = FALSE
  )
  input <- .omics$list_read_set_import_jobs_input(maxResults = maxResults, nextToken = nextToken, sequenceStoreId = sequenceStoreId, filter = filter)
  output <- .omics$list_read_set_import_jobs_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_read_set_import_jobs <- omics_list_read_set_import_jobs

#' Lists all parts in a multipart read set upload for a sequence store and
#' returns the metadata in a JSON formatted output
#'
#' @description
#' Lists all parts in a multipart read set upload for a sequence store and returns the metadata in a JSON formatted output.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_read_set_upload_parts/](https://www.paws-r-sdk.com/docs/omics_list_read_set_upload_parts/) for full documentation.
#'
#' @param sequenceStoreId &#91;required&#93; The Sequence Store ID used for the multipart uploads.
#' @param uploadId &#91;required&#93; The ID for the initiated multipart upload.
#' @param partSource &#91;required&#93; The source file for the upload part.
#' @param maxResults The maximum number of read set upload parts returned in a page.
#' @param nextToken Next token returned in the response of a previous ListReadSetUploadPartsRequest call. Used to get the next page of results.
#' @param filter Attributes used to filter for a specific subset of read set part uploads.
#'
#' @keywords internal
#'
#' @rdname omics_list_read_set_upload_parts
omics_list_read_set_upload_parts <- function(sequenceStoreId, uploadId, partSource, maxResults = NULL, nextToken = NULL, filter = NULL) {
  op <- new_operation(
    name = "ListReadSetUploadParts",
    http_method = "POST",
    http_path = "/sequencestore/{sequenceStoreId}/upload/{uploadId}/parts",
    host_prefix = "control-storage-",
    paginator = list(input_token = "nextToken", output_token = "nextToken", limit_key = "maxResults", result_key = "parts"),
    stream_api = FALSE
  )
  input <- .omics$list_read_set_upload_parts_input(sequenceStoreId = sequenceStoreId, uploadId = uploadId, partSource = partSource, maxResults = maxResults, nextToken = nextToken, filter = filter)
  output <- .omics$list_read_set_upload_parts_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_read_set_upload_parts <- omics_list_read_set_upload_parts

#' Retrieves a list of read sets from a sequence store ID and returns the
#' metadata in JSON format
#'
#' @description
#' Retrieves a list of read sets from a sequence store ID and returns the metadata in JSON format.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_read_sets/](https://www.paws-r-sdk.com/docs/omics_list_read_sets/) for full documentation.
#'
#' @param sequenceStoreId &#91;required&#93; The jobs' sequence store ID.
#' @param maxResults The maximum number of read sets to return in one page of results.
#' @param nextToken Specify the pagination token from a previous request to retrieve the next page of results.
#' @param filter A filter to apply to the list.
#'
#' @keywords internal
#'
#' @rdname omics_list_read_sets
omics_list_read_sets <- function(sequenceStoreId, maxResults = NULL, nextToken = NULL, filter = NULL) {
  op <- new_operation(
    name = "ListReadSets",
    http_method = "POST",
    http_path = "/sequencestore/{sequenceStoreId}/readsets",
    host_prefix = "control-storage-",
    paginator = list(input_token = "nextToken", output_token = "nextToken", limit_key = "maxResults", result_key = "readSets"),
    stream_api = FALSE
  )
  input <- .omics$list_read_sets_input(sequenceStoreId = sequenceStoreId, maxResults = maxResults, nextToken = nextToken, filter = filter)
  output <- .omics$list_read_sets_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_read_sets <- omics_list_read_sets

#' Retrieves the metadata of one or more reference import jobs for a
#' reference store
#'
#' @description
#' Retrieves the metadata of one or more reference import jobs for a reference store.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_reference_import_jobs/](https://www.paws-r-sdk.com/docs/omics_list_reference_import_jobs/) for full documentation.
#'
#' @param maxResults The maximum number of jobs to return in one page of results.
#' @param nextToken Specify the pagination token from a previous request to retrieve the next page of results.
#' @param referenceStoreId &#91;required&#93; The job's reference store ID.
#' @param filter A filter to apply to the list.
#'
#' @keywords internal
#'
#' @rdname omics_list_reference_import_jobs
omics_list_reference_import_jobs <- function(maxResults = NULL, nextToken = NULL, referenceStoreId, filter = NULL) {
  op <- new_operation(
    name = "ListReferenceImportJobs",
    http_method = "POST",
    http_path = "/referencestore/{referenceStoreId}/importjobs",
    host_prefix = "control-storage-",
    paginator = list(input_token = "nextToken", output_token = "nextToken", limit_key = "maxResults", result_key = "importJobs"),
    stream_api = FALSE
  )
  input <- .omics$list_reference_import_jobs_input(maxResults = maxResults, nextToken = nextToken, referenceStoreId = referenceStoreId, filter = filter)
  output <- .omics$list_reference_import_jobs_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_reference_import_jobs <- omics_list_reference_import_jobs

#' Retrieves a list of reference stores linked to your account and returns
#' their metadata in JSON format
#'
#' @description
#' Retrieves a list of reference stores linked to your account and returns their metadata in JSON format.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_reference_stores/](https://www.paws-r-sdk.com/docs/omics_list_reference_stores/) for full documentation.
#'
#' @param maxResults The maximum number of stores to return in one page of results.
#' @param nextToken Specify the pagination token from a previous request to retrieve the next page of results.
#' @param filter A filter to apply to the list.
#'
#' @keywords internal
#'
#' @rdname omics_list_reference_stores
omics_list_reference_stores <- function(maxResults = NULL, nextToken = NULL, filter = NULL) {
  op <- new_operation(
    name = "ListReferenceStores",
    http_method = "POST",
    http_path = "/referencestores",
    host_prefix = "control-storage-",
    paginator = list(input_token = "nextToken", output_token = "nextToken", limit_key = "maxResults", result_key = "referenceStores"),
    stream_api = FALSE
  )
  input <- .omics$list_reference_stores_input(maxResults = maxResults, nextToken = nextToken, filter = filter)
  output <- .omics$list_reference_stores_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_reference_stores <- omics_list_reference_stores

#' Retrieves the metadata of one or more reference genomes in a reference
#' store
#'
#' @description
#' Retrieves the metadata of one or more reference genomes in a reference store.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_references/](https://www.paws-r-sdk.com/docs/omics_list_references/) for full documentation.
#'
#' @param referenceStoreId &#91;required&#93; The references' reference store ID.
#' @param maxResults The maximum number of references to return in one page of results.
#' @param nextToken Specify the pagination token from a previous request to retrieve the next page of results.
#' @param filter A filter to apply to the list.
#'
#' @keywords internal
#'
#' @rdname omics_list_references
omics_list_references <- function(referenceStoreId, maxResults = NULL, nextToken = NULL, filter = NULL) {
  op <- new_operation(
    name = "ListReferences",
    http_method = "POST",
    http_path = "/referencestore/{referenceStoreId}/references",
    host_prefix = "control-storage-",
    paginator = list(input_token = "nextToken", output_token = "nextToken", limit_key = "maxResults", result_key = "references"),
    stream_api = FALSE
  )
  input <- .omics$list_references_input(referenceStoreId = referenceStoreId, maxResults = maxResults, nextToken = nextToken, filter = filter)
  output <- .omics$list_references_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_references <- omics_list_references

#' Retrieves a list of your run caches and the metadata for each cache
#'
#' @description
#' Retrieves a list of your run caches and the metadata for each cache.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_run_caches/](https://www.paws-r-sdk.com/docs/omics_list_run_caches/) for full documentation.
#'
#' @param maxResults The maximum number of results to return.
#' @param startingToken Optional pagination token returned from a prior call to the [`list_run_caches`][omics_list_run_caches] API operation.
#'
#' @keywords internal
#'
#' @rdname omics_list_run_caches
omics_list_run_caches <- function(maxResults = NULL, startingToken = NULL) {
  op <- new_operation(
    name = "ListRunCaches",
    http_method = "GET",
    http_path = "/runCache",
    host_prefix = "workflows-",
    paginator = list(input_token = "startingToken", output_token = "nextToken", limit_key = "maxResults", result_key = "items"),
    stream_api = FALSE
  )
  input <- .omics$list_run_caches_input(maxResults = maxResults, startingToken = startingToken)
  output <- .omics$list_run_caches_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_run_caches <- omics_list_run_caches

#' Retrieves a list of all run groups and returns the metadata for each run
#' group
#'
#' @description
#' Retrieves a list of all run groups and returns the metadata for each run group.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_run_groups/](https://www.paws-r-sdk.com/docs/omics_list_run_groups/) for full documentation.
#'
#' @param name The run groups' name.
#' @param startingToken Specify the pagination token from a previous request to retrieve the next page of results.
#' @param maxResults The maximum number of run groups to return in one page of results.
#'
#' @keywords internal
#'
#' @rdname omics_list_run_groups
omics_list_run_groups <- function(name = NULL, startingToken = NULL, maxResults = NULL) {
  op <- new_operation(
    name = "ListRunGroups",
    http_method = "GET",
    http_path = "/runGroup",
    host_prefix = "workflows-",
    paginator = list(input_token = "startingToken", output_token = "nextToken", limit_key = "maxResults", result_key = "items"),
    stream_api = FALSE
  )
  input <- .omics$list_run_groups_input(name = name, startingToken = startingToken, maxResults = maxResults)
  output <- .omics$list_run_groups_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_run_groups <- omics_list_run_groups

#' Returns a list of tasks and status information within their specified
#' run
#'
#' @description
#' 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.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_run_tasks/](https://www.paws-r-sdk.com/docs/omics_list_run_tasks/) for full documentation.
#'
#' @param id &#91;required&#93; The run's ID.
#' @param status Filter the list by status.
#' @param startingToken Specify the pagination token from a previous request to retrieve the next page of results.
#' @param maxResults The maximum number of run tasks to return in one page of results.
#'
#' @keywords internal
#'
#' @rdname omics_list_run_tasks
omics_list_run_tasks <- function(id, status = NULL, startingToken = NULL, maxResults = NULL) {
  op <- new_operation(
    name = "ListRunTasks",
    http_method = "GET",
    http_path = "/run/{id}/task",
    host_prefix = "workflows-",
    paginator = list(input_token = "startingToken", output_token = "nextToken", limit_key = "maxResults", result_key = "items"),
    stream_api = FALSE
  )
  input <- .omics$list_run_tasks_input(id = id, status = status, startingToken = startingToken, maxResults = maxResults)
  output <- .omics$list_run_tasks_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_run_tasks <- omics_list_run_tasks

#' Retrieves a list of runs and returns each run's metadata and status
#'
#' @description
#' Retrieves a list of runs and returns each run's metadata and status.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_runs/](https://www.paws-r-sdk.com/docs/omics_list_runs/) for full documentation.
#'
#' @param name Filter the list by run name.
#' @param runGroupId Filter the list by run group ID.
#' @param batchId Filter by batch ID.
#' @param startingToken Specify the pagination token from a previous request to retrieve the next page of results.
#' @param maxResults The maximum number of runs to return in one page of results.
#' @param status The status of a run.
#'
#' @keywords internal
#'
#' @rdname omics_list_runs
omics_list_runs <- function(name = NULL, runGroupId = NULL, batchId = NULL, startingToken = NULL, maxResults = NULL, status = NULL) {
  op <- new_operation(
    name = "ListRuns",
    http_method = "GET",
    http_path = "/run",
    host_prefix = "workflows-",
    paginator = list(input_token = "startingToken", output_token = "nextToken", limit_key = "maxResults", result_key = "items"),
    stream_api = FALSE
  )
  input <- .omics$list_runs_input(name = name, runGroupId = runGroupId, batchId = batchId, startingToken = startingToken, maxResults = maxResults, status = status)
  output <- .omics$list_runs_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_runs <- omics_list_runs

#' Returns a paginated list of individual workflow runs within a specific
#' batch
#'
#' @description
#' Returns a paginated list of individual workflow runs within a specific batch. Use this operation to map each `runSettingId` to its HealthOmics-generated `runId`, and to check the submission status of each run. Only one filter per call is supported.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_runs_in_batch/](https://www.paws-r-sdk.com/docs/omics_list_runs_in_batch/) for full documentation.
#'
#' @param batchId &#91;required&#93; The identifier portion of the run batch ARN.
#' @param maxItems The maximum number of runs to return.
#' @param startingToken A pagination token returned from a prior [`list_runs_in_batch`][omics_list_runs_in_batch] call.
#' @param submissionStatus Filter runs by submission status.
#' @param runSettingId Filter runs by the customer-provided run setting ID.
#' @param runId Filter runs by the HealthOmics-generated run ID.
#'
#' @keywords internal
#'
#' @rdname omics_list_runs_in_batch
omics_list_runs_in_batch <- function(batchId, maxItems = NULL, startingToken = NULL, submissionStatus = NULL, runSettingId = NULL, runId = NULL) {
  op <- new_operation(
    name = "ListRunsInBatch",
    http_method = "GET",
    http_path = "/runBatch/{batchId}/run",
    host_prefix = "workflows-",
    paginator = list(input_token = "startingToken", output_token = "nextToken", limit_key = "maxItems", result_key = "runs"),
    stream_api = FALSE
  )
  input <- .omics$list_runs_in_batch_input(batchId = batchId, maxItems = maxItems, startingToken = startingToken, submissionStatus = submissionStatus, runSettingId = runSettingId, runId = runId)
  output <- .omics$list_runs_in_batch_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_runs_in_batch <- omics_list_runs_in_batch

#' Retrieves a list of sequence stores and returns each sequence store's
#' metadata
#'
#' @description
#' Retrieves a list of sequence stores and returns each sequence store's metadata.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_sequence_stores/](https://www.paws-r-sdk.com/docs/omics_list_sequence_stores/) for full documentation.
#'
#' @param maxResults The maximum number of stores to return in one page of results.
#' @param nextToken Specify the pagination token from a previous request to retrieve the next page of results.
#' @param filter A filter to apply to the list.
#'
#' @keywords internal
#'
#' @rdname omics_list_sequence_stores
omics_list_sequence_stores <- function(maxResults = NULL, nextToken = NULL, filter = NULL) {
  op <- new_operation(
    name = "ListSequenceStores",
    http_method = "POST",
    http_path = "/sequencestores",
    host_prefix = "control-storage-",
    paginator = list(input_token = "nextToken", output_token = "nextToken", limit_key = "maxResults", result_key = "sequenceStores"),
    stream_api = FALSE
  )
  input <- .omics$list_sequence_stores_input(maxResults = maxResults, nextToken = nextToken, filter = filter)
  output <- .omics$list_sequence_stores_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_sequence_stores <- omics_list_sequence_stores

#' Retrieves the resource shares associated with an account
#'
#' @description
#' Retrieves the resource shares associated with an account. Use the filter parameter to retrieve a specific subset of the shares.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_shares/](https://www.paws-r-sdk.com/docs/omics_list_shares/) for full documentation.
#'
#' @param resourceOwner &#91;required&#93; The account that owns the resource shares.
#' @param filter Attributes that you use to filter for a specific subset of resource shares.
#' @param nextToken Next token returned in the response of a previous ListReadSetUploadPartsRequest call. Used to get the next page of results.
#' @param maxResults The maximum number of shares to return in one page of results.
#'
#' @keywords internal
#'
#' @rdname omics_list_shares
omics_list_shares <- function(resourceOwner, filter = NULL, nextToken = NULL, maxResults = NULL) {
  op <- new_operation(
    name = "ListShares",
    http_method = "POST",
    http_path = "/shares",
    host_prefix = "analytics-",
    paginator = list(input_token = "nextToken", output_token = "nextToken", limit_key = "maxResults", result_key = "shares"),
    stream_api = FALSE
  )
  input <- .omics$list_shares_input(resourceOwner = resourceOwner, filter = filter, nextToken = nextToken, maxResults = maxResults)
  output <- .omics$list_shares_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_shares <- omics_list_shares

#' Retrieves a list of tags for a resource
#'
#' @description
#' Retrieves a list of tags for a resource.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_tags_for_resource/](https://www.paws-r-sdk.com/docs/omics_list_tags_for_resource/) for full documentation.
#'
#' @param resourceArn &#91;required&#93; The resource's ARN.
#'
#' @keywords internal
#'
#' @rdname omics_list_tags_for_resource
omics_list_tags_for_resource <- function(resourceArn) {
  op <- new_operation(
    name = "ListTagsForResource",
    http_method = "GET",
    http_path = "/tags/{resourceArn}",
    host_prefix = "tags-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$list_tags_for_resource_input(resourceArn = resourceArn)
  output <- .omics$list_tags_for_resource_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_tags_for_resource <- omics_list_tags_for_resource

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_variant_import_jobs/](https://www.paws-r-sdk.com/docs/omics_list_variant_import_jobs/) for full documentation.
#'
#' @param maxResults The maximum number of import jobs to return in one page of results.
#' @param ids A list of job IDs.
#' @param nextToken Specify the pagination token from a previous request to retrieve the next page of results.
#' @param filter A filter to apply to the list.
#'
#' @keywords internal
#'
#' @rdname omics_list_variant_import_jobs
omics_list_variant_import_jobs <- function(maxResults = NULL, ids = NULL, nextToken = NULL, filter = NULL) {
  op <- new_operation(
    name = "ListVariantImportJobs",
    http_method = "POST",
    http_path = "/import/variants",
    host_prefix = "analytics-",
    paginator = list(input_token = "nextToken", output_token = "nextToken", limit_key = "maxResults", result_key = "variantImportJobs"),
    stream_api = FALSE
  )
  input <- .omics$list_variant_import_jobs_input(maxResults = maxResults, ids = ids, nextToken = nextToken, filter = filter)
  output <- .omics$list_variant_import_jobs_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_variant_import_jobs <- omics_list_variant_import_jobs

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_variant_stores/](https://www.paws-r-sdk.com/docs/omics_list_variant_stores/) for full documentation.
#'
#' @param maxResults The maximum number of stores to return in one page of results.
#' @param ids A list of store IDs.
#' @param nextToken Specify the pagination token from a previous request to retrieve the next page of results.
#' @param filter A filter to apply to the list.
#'
#' @keywords internal
#'
#' @rdname omics_list_variant_stores
omics_list_variant_stores <- function(maxResults = NULL, ids = NULL, nextToken = NULL, filter = NULL) {
  op <- new_operation(
    name = "ListVariantStores",
    http_method = "POST",
    http_path = "/variantStores",
    host_prefix = "analytics-",
    paginator = list(input_token = "nextToken", output_token = "nextToken", limit_key = "maxResults", result_key = "variantStores"),
    stream_api = FALSE
  )
  input <- .omics$list_variant_stores_input(maxResults = maxResults, ids = ids, nextToken = nextToken, filter = filter)
  output <- .omics$list_variant_stores_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_variant_stores <- omics_list_variant_stores

#' Lists the workflow versions for the specified workflow
#'
#' @description
#' Lists the workflow versions for the specified workflow. For more information, see [Workflow versioning in Amazon Web Services HealthOmics](https://docs.aws.amazon.com/omics/latest/dev/workflow-versions.html) in the *Amazon Web Services HealthOmics User Guide*.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_workflow_versions/](https://www.paws-r-sdk.com/docs/omics_list_workflow_versions/) for full documentation.
#'
#' @param workflowId &#91;required&#93; The workflow's ID. The `workflowId` is not the UUID.
#' @param type The workflow type.
#' @param workflowOwnerId The 12-digit account ID of the workflow owner. The workflow owner ID can be retrieved using the [`get_share`][omics_get_share] API operation. If you are the workflow owner, you do not need to include this ID.
#' @param startingToken Specify the pagination token from a previous request to retrieve the next page of results.
#' @param maxResults The maximum number of workflows to return in one page of results.
#'
#' @keywords internal
#'
#' @rdname omics_list_workflow_versions
omics_list_workflow_versions <- function(workflowId, type = NULL, workflowOwnerId = NULL, startingToken = NULL, maxResults = NULL) {
  op <- new_operation(
    name = "ListWorkflowVersions",
    http_method = "GET",
    http_path = "/workflow/{workflowId}/version",
    host_prefix = "workflows-",
    paginator = list(input_token = "startingToken", output_token = "nextToken", limit_key = "maxResults", result_key = "items"),
    stream_api = FALSE
  )
  input <- .omics$list_workflow_versions_input(workflowId = workflowId, type = type, workflowOwnerId = workflowOwnerId, startingToken = startingToken, maxResults = maxResults)
  output <- .omics$list_workflow_versions_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_workflow_versions <- omics_list_workflow_versions

#' Retrieves a list of existing workflows
#'
#' @description
#' 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.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_list_workflows/](https://www.paws-r-sdk.com/docs/omics_list_workflows/) for full documentation.
#'
#' @param type Filter the list by workflow type.
#' @param name Filter the list by workflow name.
#' @param startingToken Specify the pagination token from a previous request to retrieve the next page of results.
#' @param maxResults The maximum number of workflows to return in one page of results.
#'
#' @keywords internal
#'
#' @rdname omics_list_workflows
omics_list_workflows <- function(type = NULL, name = NULL, startingToken = NULL, maxResults = NULL) {
  op <- new_operation(
    name = "ListWorkflows",
    http_method = "GET",
    http_path = "/workflow",
    host_prefix = "workflows-",
    paginator = list(input_token = "startingToken", output_token = "nextToken", limit_key = "maxResults", result_key = "items"),
    stream_api = FALSE
  )
  input <- .omics$list_workflows_input(type = type, name = name, startingToken = startingToken, maxResults = maxResults)
  output <- .omics$list_workflows_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$list_workflows <- omics_list_workflows

#' Adds an access policy to the specified store
#'
#' @description
#' Adds an access policy to the specified store.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_put_s3_access_policy/](https://www.paws-r-sdk.com/docs/omics_put_s3_access_policy/) for full documentation.
#'
#' @param s3AccessPointArn &#91;required&#93; The S3 access point ARN where you want to put the access policy.
#' @param s3AccessPolicy &#91;required&#93; The resource policy that controls S3 access to the store.
#'
#' @keywords internal
#'
#' @rdname omics_put_s3_access_policy
omics_put_s3_access_policy <- function(s3AccessPointArn, s3AccessPolicy) {
  op <- new_operation(
    name = "PutS3AccessPolicy",
    http_method = "PUT",
    http_path = "/s3accesspolicy/{s3AccessPointArn}",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$put_s3_access_policy_input(s3AccessPointArn = s3AccessPointArn, s3AccessPolicy = s3AccessPolicy)
  output <- .omics$put_s3_access_policy_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$put_s3_access_policy <- omics_put_s3_access_policy

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_start_annotation_import_job/](https://www.paws-r-sdk.com/docs/omics_start_annotation_import_job/) for full documentation.
#'
#' @param destinationName &#91;required&#93; A destination annotation store for the job.
#' @param roleArn &#91;required&#93; A service role for the job.
#' @param items &#91;required&#93; Items to import.
#' @param versionName The name of the annotation store version.
#' @param formatOptions Formatting options for the annotation file.
#' @param runLeftNormalization The job's left normalization setting.
#' @param annotationFields The annotation schema generated by the parsed annotation data.
#'
#' @keywords internal
#'
#' @rdname omics_start_annotation_import_job
omics_start_annotation_import_job <- function(destinationName, roleArn, items, versionName = NULL, formatOptions = NULL, runLeftNormalization = NULL, annotationFields = NULL) {
  op <- new_operation(
    name = "StartAnnotationImportJob",
    http_method = "POST",
    http_path = "/import/annotation",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$start_annotation_import_job_input(destinationName = destinationName, roleArn = roleArn, items = items, versionName = versionName, formatOptions = formatOptions, runLeftNormalization = runLeftNormalization, annotationFields = annotationFields)
  output <- .omics$start_annotation_import_job_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$start_annotation_import_job <- omics_start_annotation_import_job

#' Activates an archived read set and returns its metadata in a JSON
#' formatted output
#'
#' @description
#' Activates an archived read set and returns its metadata in a JSON formatted output. AWS HealthOmics automatically archives unused read sets after 30 days. To monitor the status of your read set activation job, use the [`get_read_set_activation_job`][omics_get_read_set_activation_job] operation.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_start_read_set_activation_job/](https://www.paws-r-sdk.com/docs/omics_start_read_set_activation_job/) for full documentation.
#'
#' @param sequenceStoreId &#91;required&#93; The read set's sequence store ID.
#' @param clientToken To ensure that jobs don't run multiple times, specify a unique token for each job.
#' @param sources &#91;required&#93; The job's source files.
#'
#' @keywords internal
#'
#' @rdname omics_start_read_set_activation_job
omics_start_read_set_activation_job <- function(sequenceStoreId, clientToken = NULL, sources) {
  op <- new_operation(
    name = "StartReadSetActivationJob",
    http_method = "POST",
    http_path = "/sequencestore/{sequenceStoreId}/activationjob",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$start_read_set_activation_job_input(sequenceStoreId = sequenceStoreId, clientToken = clientToken, sources = sources)
  output <- .omics$start_read_set_activation_job_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$start_read_set_activation_job <- omics_start_read_set_activation_job

#' Starts a read set export job
#'
#' @description
#' Starts a read set export job. When the export job is finished, the read set is exported to an Amazon S3 bucket which can be retrieved using the [`get_read_set_export_job`][omics_get_read_set_export_job] API operation.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_start_read_set_export_job/](https://www.paws-r-sdk.com/docs/omics_start_read_set_export_job/) for full documentation.
#'
#' @param sequenceStoreId &#91;required&#93; The read set's sequence store ID.
#' @param destination &#91;required&#93; A location for exported files in Amazon S3.
#' @param roleArn &#91;required&#93; A service role for the job.
#' @param clientToken To ensure that jobs don't run multiple times, specify a unique token for each job.
#' @param sources &#91;required&#93; The job's source files.
#'
#' @keywords internal
#'
#' @rdname omics_start_read_set_export_job
omics_start_read_set_export_job <- function(sequenceStoreId, destination, roleArn, clientToken = NULL, sources) {
  op <- new_operation(
    name = "StartReadSetExportJob",
    http_method = "POST",
    http_path = "/sequencestore/{sequenceStoreId}/exportjob",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$start_read_set_export_job_input(sequenceStoreId = sequenceStoreId, destination = destination, roleArn = roleArn, clientToken = clientToken, sources = sources)
  output <- .omics$start_read_set_export_job_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$start_read_set_export_job <- omics_start_read_set_export_job

#' Imports a read set from the sequence store
#'
#' @description
#' Imports a read set from the sequence store. Read set import jobs support a maximum of 100 read sets of different types. Monitor the progress of your read set import job by calling the [`get_read_set_import_job`][omics_get_read_set_import_job] API operation.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_start_read_set_import_job/](https://www.paws-r-sdk.com/docs/omics_start_read_set_import_job/) for full documentation.
#'
#' @param sequenceStoreId &#91;required&#93; The read set's sequence store ID.
#' @param roleArn &#91;required&#93; A service role for the job.
#' @param clientToken To ensure that jobs don't run multiple times, specify a unique token for each job.
#' @param sources &#91;required&#93; The job's source files.
#'
#' @keywords internal
#'
#' @rdname omics_start_read_set_import_job
omics_start_read_set_import_job <- function(sequenceStoreId, roleArn, clientToken = NULL, sources) {
  op <- new_operation(
    name = "StartReadSetImportJob",
    http_method = "POST",
    http_path = "/sequencestore/{sequenceStoreId}/importjob",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$start_read_set_import_job_input(sequenceStoreId = sequenceStoreId, roleArn = roleArn, clientToken = clientToken, sources = sources)
  output <- .omics$start_read_set_import_job_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$start_read_set_import_job <- omics_start_read_set_import_job

#' Imports a reference genome from Amazon S3 into a specified reference
#' store
#'
#' @description
#' Imports a reference genome from Amazon S3 into a specified reference store. You can have multiple reference genomes in a reference store. You can only import reference genomes one at a time into each reference store. Monitor the status of your reference import job by using the [`get_reference_import_job`][omics_get_reference_import_job] API operation.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_start_reference_import_job/](https://www.paws-r-sdk.com/docs/omics_start_reference_import_job/) for full documentation.
#'
#' @param referenceStoreId &#91;required&#93; The job's reference store ID.
#' @param roleArn &#91;required&#93; A service role for the job.
#' @param clientToken To ensure that jobs don't run multiple times, specify a unique token for each job.
#' @param sources &#91;required&#93; The job's source files.
#'
#' @keywords internal
#'
#' @rdname omics_start_reference_import_job
omics_start_reference_import_job <- function(referenceStoreId, roleArn, clientToken = NULL, sources) {
  op <- new_operation(
    name = "StartReferenceImportJob",
    http_method = "POST",
    http_path = "/referencestore/{referenceStoreId}/importjob",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$start_reference_import_job_input(referenceStoreId = referenceStoreId, roleArn = roleArn, clientToken = clientToken, sources = sources)
  output <- .omics$start_reference_import_job_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$start_reference_import_job <- omics_start_reference_import_job

#' Starts a new run and returns details about the run, or duplicates an
#' existing run
#'
#' @description
#' Starts a new run and returns details about the run, or duplicates an existing run. A run is a single invocation of a workflow. If you provide request IDs, Amazon Web Services HealthOmics identifies duplicate requests and starts the run only once. Monitor the progress of the run by calling the [`get_run`][omics_get_run] API operation.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_start_run/](https://www.paws-r-sdk.com/docs/omics_start_run/) for full documentation.
#'
#' @param workflowId The run's workflow ID. The `workflowId` is not the UUID.
#' @param workflowType The run's workflow type. The `workflowType` must be specified if you are running a `READY2RUN` workflow. If you are running a `PRIVATE` workflow (default), you do not need to include the workflow type.
#' @param runId The ID of a run to duplicate.
#' @param roleArn &#91;required&#93; A service role for the run. The `roleArn` requires access to Amazon Web Services HealthOmics, S3, Cloudwatch logs, and EC2. An example `roleArn` is `arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ`. In this example, the AWS account ID is `123456789012` and the role name is `omics-service-role-serviceRole-W8O1XMPL7QZ`.
#' @param name A name for the run. This is recommended to view and organize runs in the Amazon Web Services HealthOmics console and CloudWatch logs.
#' @param cacheId Identifier of the cache associated with this run. If you don't specify a cache ID, no task outputs are cached for this run.
#' @param cacheBehavior The cache behavior for the run. You specify this value if you want to override the default behavior for the cache. You had set the default value when you created the cache. For more information, see [Run cache behavior](https://docs.aws.amazon.com/omics/latest/dev/how-run-cache.html#run-cache-behavior) in the *Amazon Web Services HealthOmics User Guide*.
#' @param runGroupId The run's group ID. Use a run group to cap the compute resources (and number of concurrent runs) for the runs that you add to the run group.
#' @param priority Use the run priority (highest: 1) to establish the order of runs in a run group when you start a run. If multiple runs share the same priority, the run that was initiated first will have the higher priority. Runs that do not belong to a run group can be assigned a priority. The priorities of these runs are ranked among other runs that are not in a run group. For more information, see [Run priority](https://docs.aws.amazon.com/omics/latest/dev/creating-run-groups.html#run-priority) in the *Amazon Web Services HealthOmics User Guide*.
#' @param parameters Parameters for the run. The run needs all required parameters and can include optional parameters. The run cannot include any parameters that are not defined in the parameter template. To retrieve parameters from the run, use the GetRun API operation.
#' @param storageCapacity The `STATIC` storage capacity (in gibibytes, GiB) for this run. The default run storage capacity is 1200 GiB. If your requested storage capacity is unavailable, the system rounds up the value to the nearest 1200 GiB multiple. If the requested storage capacity is still unavailable, the system rounds up the value to the nearest 2400 GiB multiple. This field is not required if the storage type is `DYNAMIC` (the system ignores any value that you enter).
#' @param outputUri &#91;required&#93; An output S3 URI for the run. The S3 bucket must be in the same region as the workflow. The role ARN must have permission to write to this S3 bucket.
#' @param logLevel A log level for the run.
#' @param tags Tags for the run. You can add up to 50 tags per run. For more information, see [Adding a tag](https://docs.aws.amazon.com/omics/latest/dev/add-a-tag.html) in the *Amazon Web Services HealthOmics User Guide*.
#' @param requestId &#91;required&#93; An idempotency token used to dedupe retry requests so that duplicate runs are not created.
#' @param retentionMode The retention mode for the run. The default value is `RETAIN`.
#' 
#' Amazon Web Services HealthOmics stores a fixed number of runs that are available to the console and API. In the default mode (`RETAIN`), you need to remove runs manually when the number of run exceeds the maximum. If you set the retention mode to `REMOVE`, Amazon Web Services HealthOmics automatically removes runs (that have mode set to `REMOVE`) when the number of run exceeds the maximum. All run logs are available in CloudWatch logs, if you need information about a run that is no longer available to the API.
#' 
#' For more information about retention mode, see [Specifying run retention mode](https://docs.aws.amazon.com/omics/latest/dev/starting-a-run.html) in the *Amazon Web Services HealthOmics User Guide*.
#' @param storageType The storage type for the run. If you set the storage type to `DYNAMIC`, Amazon Web Services HealthOmics dynamically scales the storage up or down, based on file system utilization. By default, the run uses `STATIC` storage type, which allocates a fixed amount of storage. For more information about `DYNAMIC` and `STATIC` storage, see [Run storage types](https://docs.aws.amazon.com/omics/latest/dev/workflows-run-types.html) in the *Amazon Web Services HealthOmics User Guide*.
#' @param workflowOwnerId The 12-digit account ID of the workflow owner that is used for running a shared workflow. The workflow owner ID can be retrieved using the [`get_share`][omics_get_share] API operation. If you are the workflow owner, you do not need to include this ID.
#' @param workflowVersionName The name of the workflow version. Use workflow versions to track and organize changes to the workflow. If your workflow has multiple versions, the run uses the default version unless you specify a version name. To learn more, see [Workflow versioning](https://docs.aws.amazon.com/omics/latest/dev/workflow-versions.html) in the *Amazon Web Services HealthOmics User Guide*.
#' @param networkingMode Optional configuration for run networking behavior. If not specified, this will default to RESTRICTED.
#' @param configurationName Optional configuration name to use for the workflow run.
#'
#' @keywords internal
#'
#' @rdname omics_start_run
omics_start_run <- function(workflowId = NULL, workflowType = NULL, runId = NULL, roleArn, name = NULL, cacheId = NULL, cacheBehavior = NULL, runGroupId = NULL, priority = NULL, parameters = NULL, storageCapacity = NULL, outputUri, logLevel = NULL, tags = NULL, requestId, retentionMode = NULL, storageType = NULL, workflowOwnerId = NULL, workflowVersionName = NULL, networkingMode = NULL, configurationName = NULL) {
  op <- new_operation(
    name = "StartRun",
    http_method = "POST",
    http_path = "/run",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$start_run_input(workflowId = workflowId, workflowType = workflowType, runId = runId, roleArn = roleArn, name = name, cacheId = cacheId, cacheBehavior = cacheBehavior, runGroupId = runGroupId, priority = priority, parameters = parameters, storageCapacity = storageCapacity, outputUri = outputUri, logLevel = logLevel, tags = tags, requestId = requestId, retentionMode = retentionMode, storageType = storageType, workflowOwnerId = workflowOwnerId, workflowVersionName = workflowVersionName, networkingMode = networkingMode, configurationName = configurationName)
  output <- .omics$start_run_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$start_run <- omics_start_run

#' Starts a batch of workflow runs
#'
#' @description
#' Starts a batch of workflow runs. You can group up to 100,000 runs into a single batch that share a common configuration defined in `defaultRunSetting`. Per-run overrides can be provided either inline via `inlineSettings` (up to 100 runs) or via a JSON file stored in Amazon S3 via `s3UriSettings` (up to 100,000 runs).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_start_run_batch/](https://www.paws-r-sdk.com/docs/omics_start_run_batch/) for full documentation.
#'
#' @param batchName An optional user-friendly name for the run batch.
#' @param requestId &#91;required&#93; A client token used to deduplicate retry requests and prevent duplicate batches from being created.
#' @param tags AWS tags to associate with the batch resource. These tags are not inherited by individual runs. To tag individual runs, use `defaultRunSetting.runTags`.
#' @param defaultRunSetting &#91;required&#93; Shared configuration applied to all runs in the batch. See `DefaultRunSetting`.
#' @param batchRunSettings &#91;required&#93; The individual run configurations. Specify exactly one of `inlineSettings` or `s3UriSettings`. See `BatchRunSettings`.
#'
#' @keywords internal
#'
#' @rdname omics_start_run_batch
omics_start_run_batch <- function(batchName = NULL, requestId, tags = NULL, defaultRunSetting, batchRunSettings) {
  op <- new_operation(
    name = "StartRunBatch",
    http_method = "POST",
    http_path = "/runBatch",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$start_run_batch_input(batchName = batchName, requestId = requestId, tags = tags, defaultRunSetting = defaultRunSetting, batchRunSettings = batchRunSettings)
  output <- .omics$start_run_batch_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$start_run_batch <- omics_start_run_batch

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_start_variant_import_job/](https://www.paws-r-sdk.com/docs/omics_start_variant_import_job/) for full documentation.
#'
#' @param destinationName &#91;required&#93; The destination variant store for the job.
#' @param roleArn &#91;required&#93; A service role for the job.
#' @param items &#91;required&#93; Items to import.
#' @param runLeftNormalization The job's left normalization setting.
#' @param annotationFields The annotation schema generated by the parsed annotation data.
#'
#' @keywords internal
#'
#' @rdname omics_start_variant_import_job
omics_start_variant_import_job <- function(destinationName, roleArn, items, runLeftNormalization = NULL, annotationFields = NULL) {
  op <- new_operation(
    name = "StartVariantImportJob",
    http_method = "POST",
    http_path = "/import/variant",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$start_variant_import_job_input(destinationName = destinationName, roleArn = roleArn, items = items, runLeftNormalization = runLeftNormalization, annotationFields = annotationFields)
  output <- .omics$start_variant_import_job_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$start_variant_import_job <- omics_start_variant_import_job

#' Tags a resource
#'
#' @description
#' Tags a resource.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_tag_resource/](https://www.paws-r-sdk.com/docs/omics_tag_resource/) for full documentation.
#'
#' @param resourceArn &#91;required&#93; The resource's ARN.
#' @param tags &#91;required&#93; Tags for the resource.
#'
#' @keywords internal
#'
#' @rdname omics_tag_resource
omics_tag_resource <- function(resourceArn, tags) {
  op <- new_operation(
    name = "TagResource",
    http_method = "POST",
    http_path = "/tags/{resourceArn}",
    host_prefix = "tags-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$tag_resource_input(resourceArn = resourceArn, tags = tags)
  output <- .omics$tag_resource_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$tag_resource <- omics_tag_resource

#' Removes tags from a resource
#'
#' @description
#' Removes tags from a resource.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_untag_resource/](https://www.paws-r-sdk.com/docs/omics_untag_resource/) for full documentation.
#'
#' @param resourceArn &#91;required&#93; The resource's ARN.
#' @param tagKeys &#91;required&#93; Keys of tags to remove.
#'
#' @keywords internal
#'
#' @rdname omics_untag_resource
omics_untag_resource <- function(resourceArn, tagKeys) {
  op <- new_operation(
    name = "UntagResource",
    http_method = "DELETE",
    http_path = "/tags/{resourceArn}",
    host_prefix = "tags-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$untag_resource_input(resourceArn = resourceArn, tagKeys = tagKeys)
  output <- .omics$untag_resource_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$untag_resource <- omics_untag_resource

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_update_annotation_store/](https://www.paws-r-sdk.com/docs/omics_update_annotation_store/) for full documentation.
#'
#' @param name &#91;required&#93; A name for the store.
#' @param description A description for the store.
#'
#' @keywords internal
#'
#' @rdname omics_update_annotation_store
omics_update_annotation_store <- function(name, description = NULL) {
  op <- new_operation(
    name = "UpdateAnnotationStore",
    http_method = "POST",
    http_path = "/annotationStore/{name}",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$update_annotation_store_input(name = name, description = description)
  output <- .omics$update_annotation_store_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$update_annotation_store <- omics_update_annotation_store

#' Updates the description of an annotation store version
#'
#' @description
#' Updates the description of an annotation store version.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_update_annotation_store_version/](https://www.paws-r-sdk.com/docs/omics_update_annotation_store_version/) for full documentation.
#'
#' @param name &#91;required&#93; The name of an annotation store.
#' @param versionName &#91;required&#93; The name of an annotation store version.
#' @param description The description of an annotation store.
#'
#' @keywords internal
#'
#' @rdname omics_update_annotation_store_version
omics_update_annotation_store_version <- function(name, versionName, description = NULL) {
  op <- new_operation(
    name = "UpdateAnnotationStoreVersion",
    http_method = "POST",
    http_path = "/annotationStore/{name}/version/{versionName}",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$update_annotation_store_version_input(name = name, versionName = versionName, description = description)
  output <- .omics$update_annotation_store_version_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$update_annotation_store_version <- omics_update_annotation_store_version

#' Updates a run cache using its ID and returns a response with no body if
#' the operation is successful
#'
#' @description
#' 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 [`get_run_cache`][omics_get_run_cache] API operation.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_update_run_cache/](https://www.paws-r-sdk.com/docs/omics_update_run_cache/) for full documentation.
#'
#' @param cacheBehavior Update the default run cache behavior.
#' @param description Update the run cache description.
#' @param id &#91;required&#93; The identifier of the run cache you want to update.
#' @param name Update the name of the run cache.
#'
#' @keywords internal
#'
#' @rdname omics_update_run_cache
omics_update_run_cache <- function(cacheBehavior = NULL, description = NULL, id, name = NULL) {
  op <- new_operation(
    name = "UpdateRunCache",
    http_method = "POST",
    http_path = "/runCache/{id}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$update_run_cache_input(cacheBehavior = cacheBehavior, description = description, id = id, name = name)
  output <- .omics$update_run_cache_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$update_run_cache <- omics_update_run_cache

#' Updates the settings of a run group and returns a response with no body
#' if the operation is successful
#'
#' @description
#' Updates the settings of a run group and returns a response with no body if the operation is successful.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_update_run_group/](https://www.paws-r-sdk.com/docs/omics_update_run_group/) for full documentation.
#'
#' @param id &#91;required&#93; The group's ID.
#' @param name A name for the group.
#' @param maxCpus The maximum number of CPUs to use.
#' @param maxRuns The maximum number of concurrent runs for the group.
#' @param maxDuration A maximum run time for the group in minutes.
#' @param maxGpus The maximum GPUs that can be used by a run group.
#'
#' @keywords internal
#'
#' @rdname omics_update_run_group
omics_update_run_group <- function(id, name = NULL, maxCpus = NULL, maxRuns = NULL, maxDuration = NULL, maxGpus = NULL) {
  op <- new_operation(
    name = "UpdateRunGroup",
    http_method = "POST",
    http_path = "/runGroup/{id}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$update_run_group_input(id = id, name = name, maxCpus = maxCpus, maxRuns = maxRuns, maxDuration = maxDuration, maxGpus = maxGpus)
  output <- .omics$update_run_group_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$update_run_group <- omics_update_run_group

#' Update one or more parameters for the sequence store
#'
#' @description
#' Update one or more parameters for the sequence store.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_update_sequence_store/](https://www.paws-r-sdk.com/docs/omics_update_sequence_store/) for full documentation.
#'
#' @param id &#91;required&#93; The ID of the sequence store.
#' @param name A name for the sequence store.
#' @param description A description for the sequence store.
#' @param clientToken To ensure that requests don't run multiple times, specify a unique token for each request.
#' @param fallbackLocation The S3 URI of a bucket and folder to store Read Sets that fail to upload.
#' @param propagatedSetLevelTags The tags keys to propagate to the S3 objects associated with read sets in the sequence store.
#' @param s3AccessConfig S3 access configuration parameters.
#'
#' @keywords internal
#'
#' @rdname omics_update_sequence_store
omics_update_sequence_store <- function(id, name = NULL, description = NULL, clientToken = NULL, fallbackLocation = NULL, propagatedSetLevelTags = NULL, s3AccessConfig = NULL) {
  op <- new_operation(
    name = "UpdateSequenceStore",
    http_method = "PATCH",
    http_path = "/sequencestore/{id}",
    host_prefix = "control-storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$update_sequence_store_input(id = id, name = name, description = description, clientToken = clientToken, fallbackLocation = fallbackLocation, propagatedSetLevelTags = propagatedSetLevelTags, s3AccessConfig = s3AccessConfig)
  output <- .omics$update_sequence_store_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$update_sequence_store <- omics_update_sequence_store

#' Amazon Web Services HealthOmics variant stores and annotation stores are
#' no longer open to new customers
#'
#' @description
#' Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers. Existing customers can continue to use the service as normal. For more information, see [Amazon Web Services HealthOmics variant store and annotation store availability change](https://docs.aws.amazon.com/omics/latest/dev/variant-store-availability-change.html).
#'
#' See [https://www.paws-r-sdk.com/docs/omics_update_variant_store/](https://www.paws-r-sdk.com/docs/omics_update_variant_store/) for full documentation.
#'
#' @param name &#91;required&#93; A name for the store.
#' @param description A description for the store.
#'
#' @keywords internal
#'
#' @rdname omics_update_variant_store
omics_update_variant_store <- function(name, description = NULL) {
  op <- new_operation(
    name = "UpdateVariantStore",
    http_method = "POST",
    http_path = "/variantStore/{name}",
    host_prefix = "analytics-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$update_variant_store_input(name = name, description = description)
  output <- .omics$update_variant_store_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$update_variant_store <- omics_update_variant_store

#' Updates information about a workflow
#'
#' @description
#' Updates information about a workflow.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_update_workflow/](https://www.paws-r-sdk.com/docs/omics_update_workflow/) for full documentation.
#'
#' @param id &#91;required&#93; The workflow's ID.
#' @param name A name for the workflow.
#' @param description A description for the workflow.
#' @param storageType The default storage type for runs that use this workflow. STATIC storage allocates a fixed amount of storage. DYNAMIC storage dynamically scales the storage up or down, based on file system utilization. For more information about static and dynamic storage, see [Running workflows](https://docs.aws.amazon.com/omics/latest/dev/) in the *Amazon Web Services HealthOmics User Guide*.
#' @param storageCapacity The default static storage capacity (in gibibytes) for runs that use this workflow or workflow version.
#' @param readmeMarkdown The markdown content for the workflow's README file. This provides documentation and usage information for users of the workflow.
#'
#' @keywords internal
#'
#' @rdname omics_update_workflow
omics_update_workflow <- function(id, name = NULL, description = NULL, storageType = NULL, storageCapacity = NULL, readmeMarkdown = NULL) {
  op <- new_operation(
    name = "UpdateWorkflow",
    http_method = "POST",
    http_path = "/workflow/{id}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$update_workflow_input(id = id, name = name, description = description, storageType = storageType, storageCapacity = storageCapacity, readmeMarkdown = readmeMarkdown)
  output <- .omics$update_workflow_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$update_workflow <- omics_update_workflow

#' Updates information about the workflow version
#'
#' @description
#' Updates information about the workflow version. For more information, see [Workflow versioning in Amazon Web Services HealthOmics](https://docs.aws.amazon.com/omics/latest/dev/workflow-versions.html) in the *Amazon Web Services HealthOmics User Guide*.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_update_workflow_version/](https://www.paws-r-sdk.com/docs/omics_update_workflow_version/) for full documentation.
#'
#' @param workflowId &#91;required&#93; The workflow's ID. The `workflowId` is not the UUID.
#' @param versionName &#91;required&#93; The name of the workflow version.
#' @param description Description of the workflow version.
#' @param storageType The default storage type for runs that use this workflow version. The `storageType` can be overridden at run time. `DYNAMIC` storage dynamically scales the storage up or down, based on file system utilization. STATIC storage allocates a fixed amount of storage. For more information about dynamic and static storage types, see [Run storage types](https://docs.aws.amazon.com/omics/latest/dev/workflows-run-types.html) in the *in the Amazon Web Services HealthOmics User Guide* .
#' @param storageCapacity The default static storage capacity (in gibibytes) for runs that use this workflow version. The `storageCapacity` can be overwritten at run time. The storage capacity is not required for runs with a `DYNAMIC` storage type.
#' @param readmeMarkdown The markdown content for the workflow version's README file. This provides documentation and usage information for users of this specific workflow version.
#'
#' @keywords internal
#'
#' @rdname omics_update_workflow_version
omics_update_workflow_version <- function(workflowId, versionName, description = NULL, storageType = NULL, storageCapacity = NULL, readmeMarkdown = NULL) {
  op <- new_operation(
    name = "UpdateWorkflowVersion",
    http_method = "POST",
    http_path = "/workflow/{workflowId}/version/{versionName}",
    host_prefix = "workflows-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$update_workflow_version_input(workflowId = workflowId, versionName = versionName, description = description, storageType = storageType, storageCapacity = storageCapacity, readmeMarkdown = readmeMarkdown)
  output <- .omics$update_workflow_version_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$update_workflow_version <- omics_update_workflow_version

#' Uploads a specific part of a read set into a sequence store
#'
#' @description
#' Uploads a specific part of a read set into a sequence store. When you a upload a read set part with a part number that already exists, the new part replaces the existing one. This operation returns a JSON formatted response containing a string identifier that is used to confirm that parts are being added to the intended upload.
#'
#' See [https://www.paws-r-sdk.com/docs/omics_upload_read_set_part/](https://www.paws-r-sdk.com/docs/omics_upload_read_set_part/) for full documentation.
#'
#' @param sequenceStoreId &#91;required&#93; The Sequence Store ID used for the multipart upload.
#' @param uploadId &#91;required&#93; The ID for the initiated multipart upload.
#' @param partSource &#91;required&#93; The source file for an upload part.
#' @param partNumber &#91;required&#93; The number of the part being uploaded.
#' @param payload &#91;required&#93; The read set data to upload for a part.
#'
#' @keywords internal
#'
#' @rdname omics_upload_read_set_part
omics_upload_read_set_part <- function(sequenceStoreId, uploadId, partSource, partNumber, payload) {
  op <- new_operation(
    name = "UploadReadSetPart",
    http_method = "PUT",
    http_path = "/sequencestore/{sequenceStoreId}/upload/{uploadId}/part",
    host_prefix = "storage-",
    paginator = list(),
    stream_api = FALSE
  )
  input <- .omics$upload_read_set_part_input(sequenceStoreId = sequenceStoreId, uploadId = uploadId, partSource = partSource, partNumber = partNumber, payload = payload)
  output <- .omics$upload_read_set_part_output()
  config <- get_config()
  svc <- .omics$service(config, op)
  request <- new_request(svc, op, input, output)
  response <- send_request(request)
  return(response)
}
.omics$operations$upload_read_set_part <- omics_upload_read_set_part