View Source AWS.Omics (aws-elixir v1.0.6)

This is the AWS HealthOmics API Reference.

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

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Functions

Accept a resource share request.

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

Creates a new version of an annotation store.

You can create a run cache to save the task outputs from completed tasks in a run for a private workflow.

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

Creates a cross-account shared resource.

Creates a private workflow.Private workflows depend on a variety of resources that you create and configure before creating the workflow

Creates a new workflow version for the workflow that you specify with the workflowId parameter.

Deletes one or multiple versions of an annotation store.

Deletes an access policy for the specified store.

Gets information about an annotation import job.

Gets information about an annotation store.

Retrieves the metadata for an annotation store version.

Gets information about a read set activation job.

Gets information about a read set export job.

Gets information about a read set import job.

Gets information about a reference import job.

Gets information about a genome reference's metadata.

Gets information about a reference store.

Gets information about a workflow run.

Retrieve the details for the specified run cache.

Gets information about a workflow run group.

Gets information about a workflow run task.

Retrieves details about an access policy on a given store.

Gets information about a sequence store.

Retrieves the metadata for the specified resource share.

Gets information about a variant import job.

Gets information about a variant store.

Retrieves a list of annotation import jobs.

Lists the versions of an annotation store.

Retrieves a list of annotation stores.

Lists multipart read set uploads and for in progress uploads.

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

Retrieves a list of reference stores.

Retrieves a list of sequence stores.

Retrieves the resource shares associated with an account.

Retrieves a list of tags for a resource.

Retrieves a list of variant import jobs.

Retrieves a list of variant stores.

Adds an access policy to the specified store.

Starts a new run or duplicates an existing run.

Updates the description of an annotation store version.

Update one or more parameters for the sequence store.

Updates information about a workflow.

This operation uploads a specific part of a read set.

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abort_multipart_read_set_upload(client, sequence_store_id, upload_id, input, options \\ [])

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Stops a multipart upload.

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accept_share(client, share_id, input, options \\ [])

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Accept a resource share request.

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batch_delete_read_set(client, sequence_store_id, input, options \\ [])

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Deletes one or more read sets.

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cancel_annotation_import_job(client, job_id, input, options \\ [])

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Cancels an annotation import job.

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cancel_run(client, id, input, options \\ [])

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Cancels a run.

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cancel_variant_import_job(client, job_id, input, options \\ [])

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Cancels a variant import job.

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complete_multipart_read_set_upload(client, sequence_store_id, upload_id, input, options \\ [])

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

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create_annotation_store(client, input, options \\ [])

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Creates an annotation store.

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create_annotation_store_version(client, name, input, options \\ [])

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Creates a new version of an annotation store.

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create_multipart_read_set_upload(client, sequence_store_id, input, options \\ [])

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Begins a multipart read set upload.

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create_reference_store(client, input, options \\ [])

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Creates a reference store.

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create_run_cache(client, input, options \\ [])

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You can create a run cache to save the task outputs from completed tasks in a run for a private workflow.

Subsequent runs use the task outputs from the cache, rather than computing the task outputs again. You specify an Amazon S3 location where Amazon Web Services HealthOmics saves the cached data. This data must be immediately accessible (not in an archived state).

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

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create_run_group(client, input, options \\ [])

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

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create_sequence_store(client, input, options \\ [])

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Creates a sequence store.

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create_share(client, input, options \\ [])

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Creates a cross-account shared resource.

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

The following resources support cross-account sharing:

  • HealthOmics variant stores

  • HealthOmics annotation stores

  • Private workflows

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create_variant_store(client, input, options \\ [])

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Creates a variant store.

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create_workflow(client, input, options \\ [])

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Creates a private workflow.Private workflows depend on a variety of resources that you create and configure before creating the workflow:

  • Input data: Input data for the workflow, stored in an S3 bucket or a Amazon Web Services HealthOmics sequence store.

  • Workflow definition files: Define your workflow in one or more workflow definition files, written in WDL, Nextflow, or CWL. The workflow definition specifies the inputs and outputs for runs that use the workflow. It also includes specifications for the runs and run tasks for your workflow, including compute and memory requirements.

  • Parameter template files: Define run parameters using a parameter template file (written in JSON).

  • ECR container images: Create one or more container images for the workflow. Store the images in a private ECR repository.

  • (Optional) Sentieon licenses: Request a Sentieon license if you plan to use Sentieon software in a private workflow.

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

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create_workflow_version(client, workflow_id, input, options \\ [])

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Creates a new workflow version for the workflow that you specify with the workflowId parameter.

When you create a new version of a workflow, you need to specify the configuration for the new version. It doesn't inherit any configuration values from the workflow.

Provide a version name that is unique for this workflow. You cannot change the name after HealthOmics creates the version.

Don’t include any personally identifiable information (PII) in the version name. Version names appear in the workflow version ARN.

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

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delete_annotation_store(client, name, input, options \\ [])

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Deletes an annotation store.

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delete_annotation_store_versions(client, name, input, options \\ [])

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Deletes one or multiple versions of an annotation store.

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delete_reference(client, id, reference_store_id, input, options \\ [])

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Deletes a genome reference.

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delete_reference_store(client, id, input, options \\ [])

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Deletes a genome reference store.

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delete_run(client, id, input, options \\ [])

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Deletes a workflow run.

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delete_run_cache(client, id, input, options \\ [])

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Delete a run cache.

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

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

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delete_run_group(client, id, input, options \\ [])

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Deletes a workflow run group.

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delete_s3_access_policy(client, s3_access_point_arn, input, options \\ [])

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Deletes an access policy for the specified store.

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delete_sequence_store(client, id, input, options \\ [])

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Deletes a sequence store.

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delete_share(client, share_id, input, options \\ [])

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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.

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delete_variant_store(client, name, input, options \\ [])

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Deletes a variant store.

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delete_workflow(client, id, input, options \\ [])

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Deletes a workflow.

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delete_workflow_version(client, version_name, workflow_id, input, options \\ [])

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Deletes a workflow version.

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

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

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get_annotation_import_job(client, job_id, options \\ [])

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Gets information about an annotation import job.

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get_annotation_store(client, name, options \\ [])

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Gets information about an annotation store.

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get_annotation_store_version(client, name, version_name, options \\ [])

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Retrieves the metadata for an annotation store version.

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get_read_set(client, id, sequence_store_id, file \\ nil, part_number, options \\ [])

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Gets a file from a read set.

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get_read_set_activation_job(client, id, sequence_store_id, options \\ [])

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Gets information about a read set activation job.

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get_read_set_export_job(client, id, sequence_store_id, options \\ [])

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Gets information about a read set export job.

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get_read_set_import_job(client, id, sequence_store_id, options \\ [])

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Gets information about a read set import job.

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get_read_set_metadata(client, id, sequence_store_id, options \\ [])

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Gets details about a read set.

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get_reference(client, id, reference_store_id, file \\ nil, part_number, range \\ nil, options \\ [])

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Gets a reference file.

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get_reference_import_job(client, id, reference_store_id, options \\ [])

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Gets information about a reference import job.

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get_reference_metadata(client, id, reference_store_id, options \\ [])

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Gets information about a genome reference's metadata.

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get_reference_store(client, id, options \\ [])

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Gets information about a reference store.

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get_run(client, id, export \\ nil, options \\ [])

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Gets information about a workflow run.

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

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

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get_run_cache(client, id, options \\ [])

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Retrieve the details for the specified run cache.

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

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get_run_group(client, id, options \\ [])

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Gets information about a workflow run group.

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get_run_task(client, id, task_id, options \\ [])

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Gets information about a workflow run task.

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get_s3_access_policy(client, s3_access_point_arn, options \\ [])

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Retrieves details about an access policy on a given store.

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get_sequence_store(client, id, options \\ [])

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Gets information about a sequence store.

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get_share(client, share_id, options \\ [])

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Retrieves the metadata for the specified resource share.

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get_variant_import_job(client, job_id, options \\ [])

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Gets information about a variant import job.

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get_variant_store(client, name, options \\ [])

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Gets information about a variant store.

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get_workflow(client, id, export \\ nil, type \\ nil, workflow_owner_id \\ nil, options \\ [])

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Gets information about a workflow.

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

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get_workflow_version(client, version_name, workflow_id, export \\ nil, type \\ nil, workflow_owner_id \\ nil, options \\ [])

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Gets information about a workflow version.

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

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list_annotation_import_jobs(client, input, options \\ [])

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Retrieves a list of annotation import jobs.

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list_annotation_store_versions(client, name, input, options \\ [])

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Lists the versions of an annotation store.

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list_annotation_stores(client, input, options \\ [])

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Retrieves a list of annotation stores.

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list_multipart_read_set_uploads(client, sequence_store_id, input, options \\ [])

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Lists multipart read set uploads and for in progress uploads.

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

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list_read_set_activation_jobs(client, sequence_store_id, input, options \\ [])

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Retrieves a list of read set activation jobs.

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list_read_set_export_jobs(client, sequence_store_id, input, options \\ [])

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Retrieves a list of read set export jobs.

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list_read_set_import_jobs(client, sequence_store_id, input, options \\ [])

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Retrieves a list of read set import jobs.

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list_read_set_upload_parts(client, sequence_store_id, upload_id, input, options \\ [])

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

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list_read_sets(client, sequence_store_id, input, options \\ [])

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Retrieves a list of read sets.

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list_reference_import_jobs(client, reference_store_id, input, options \\ [])

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Retrieves a list of reference import jobs.

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list_reference_stores(client, input, options \\ [])

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Retrieves a list of reference stores.

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list_references(client, reference_store_id, input, options \\ [])

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Retrieves a list of references.

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list_run_caches(client, max_results \\ nil, starting_token \\ nil, options \\ [])

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Retrieves a list of your run caches.

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list_run_groups(client, max_results \\ nil, name \\ nil, starting_token \\ nil, options \\ [])

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Retrieves a list of run groups.

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list_run_tasks(client, id, max_results \\ nil, starting_token \\ nil, status \\ nil, options \\ [])

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Retrieves a list of tasks for a run.

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list_runs(client, max_results \\ nil, name \\ nil, run_group_id \\ nil, starting_token \\ nil, status \\ nil, options \\ [])

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Retrieves a list of runs.

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

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list_sequence_stores(client, input, options \\ [])

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Retrieves a list of sequence stores.

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list_shares(client, input, options \\ [])

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Retrieves the resource shares associated with an account.

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

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list_tags_for_resource(client, resource_arn, options \\ [])

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Retrieves a list of tags for a resource.

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list_variant_import_jobs(client, input, options \\ [])

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Retrieves a list of variant import jobs.

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list_variant_stores(client, input, options \\ [])

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Retrieves a list of variant stores.

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list_workflow_versions(client, workflow_id, max_results \\ nil, starting_token \\ nil, type \\ nil, workflow_owner_id \\ nil, options \\ [])

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Lists the workflow versions for the specified workflow.

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

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list_workflows(client, max_results \\ nil, name \\ nil, starting_token \\ nil, type \\ nil, options \\ [])

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Retrieves a list of workflows.

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put_s3_access_policy(client, s3_access_point_arn, input, options \\ [])

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Adds an access policy to the specified store.

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start_annotation_import_job(client, input, options \\ [])

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Starts an annotation import job.

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start_read_set_activation_job(client, sequence_store_id, input, options \\ [])

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Activates an archived read set.

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

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start_read_set_export_job(client, sequence_store_id, input, options \\ [])

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Exports a read set to Amazon S3.

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start_read_set_import_job(client, sequence_store_id, input, options \\ [])

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Starts a read set import job.

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start_reference_import_job(client, reference_store_id, input, options \\ [])

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Starts a reference import job.

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start_run(client, input, options \\ [])

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Starts a new run or duplicates an existing run.

For a new run, specify a unique requestId, the workflowId, and a role ARN. If you're using static run storage (the default), specify the required storageCapacity.

You duplicate a run by specifing a unique requestId, the runID of the run to duplicate, and a role ARN.

For more information about the optional parameters in the StartRun request, see Starting a run in the Amazon Web Services HealthOmics User Guide.

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start_variant_import_job(client, input, options \\ [])

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Starts a variant import job.

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tag_resource(client, resource_arn, input, options \\ [])

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Tags a resource.

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untag_resource(client, resource_arn, input, options \\ [])

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Removes tags from a resource.

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update_annotation_store(client, name, input, options \\ [])

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Updates an annotation store.

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update_annotation_store_version(client, name, version_name, input, options \\ [])

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Updates the description of an annotation store version.

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update_run_cache(client, id, input, options \\ [])

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Update a run cache.

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update_run_group(client, id, input, options \\ [])

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Updates a run group.

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update_sequence_store(client, id, input, options \\ [])

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Update one or more parameters for the sequence store.

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update_variant_store(client, name, input, options \\ [])

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Updates a variant store.

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update_workflow(client, id, input, options \\ [])

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Updates information about a workflow.

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

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update_workflow_version(client, version_name, workflow_id, input, options \\ [])

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Updates information about the workflow version.

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

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upload_read_set_part(client, sequence_store_id, upload_id, input, options \\ [])

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This operation uploads a specific part of a read set.

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