feat(client-omics): Add Git integration and README support for HealthOmics workflows

Author: awstools

clients/client-omics/README.md

@@ -6,7 +6,7 @@
 
 AWS SDK for JavaScript Omics Client for Node.js, Browser and React Native.
 
-<p>This is the <i>AWS HealthOmics API Reference</i>. For an introduction to the service, see <a href="https://docs.aws.amazon.com/omics/latest/dev/">What is AWS HealthOmics?</a> in the <i>AWS HealthOmics User Guide</i>.</p>
+<p>Amazon Web Services HealthOmics is a service that helps users such as bioinformaticians, researchers, and scientists to store, query, analyze, and generate insights from genomics and other biological data. It simplifies and accelerates the process of storing and analyzing genomic information for Amazon Web Services.</p> <p>For an introduction to the service, see <a href="https://docs.aws.amazon.com/omics/latest/dev/what-is-healthomics.html">What is Amazon Web Services HealthOmics?</a> in the <i>Amazon Web Services HealthOmics User Guide</i>.</p>
 
 ## Installing
 

clients/client-omics/src/Omics.ts

@@ -1990,7 +1990,7 @@ export interface Omics {
 }
 
 /**
- * <p>This is the <i>AWS HealthOmics API Reference</i>. For an introduction to the service, see <a href="https://docs.aws.amazon.com/omics/latest/dev/">What is AWS HealthOmics?</a> in the <i>AWS HealthOmics User Guide</i>.</p>
+ * <p>Amazon Web Services HealthOmics is a service that helps users such as bioinformaticians, researchers, and scientists to store, query, analyze, and generate insights from genomics and other biological data. It simplifies and accelerates the process of storing and analyzing genomic information for Amazon Web Services.</p> <p>For an introduction to the service, see <a href="https://docs.aws.amazon.com/omics/latest/dev/what-is-healthomics.html">What is Amazon Web Services HealthOmics?</a> in the <i>Amazon Web Services HealthOmics User Guide</i>.</p>
  * @public
  */
 export class Omics extends OmicsClient implements Omics {}

clients/client-omics/src/OmicsClient.ts

@@ -701,7 +701,7 @@ export type OmicsClientResolvedConfigType = __SmithyResolvedConfiguration<__Http
 export interface OmicsClientResolvedConfig extends OmicsClientResolvedConfigType {}
 
 /**
- * <p>This is the <i>AWS HealthOmics API Reference</i>. For an introduction to the service, see <a href="https://docs.aws.amazon.com/omics/latest/dev/">What is AWS HealthOmics?</a> in the <i>AWS HealthOmics User Guide</i>.</p>
+ * <p>Amazon Web Services HealthOmics is a service that helps users such as bioinformaticians, researchers, and scientists to store, query, analyze, and generate insights from genomics and other biological data. It simplifies and accelerates the process of storing and analyzing genomic information for Amazon Web Services.</p> <p>For an introduction to the service, see <a href="https://docs.aws.amazon.com/omics/latest/dev/what-is-healthomics.html">What is Amazon Web Services HealthOmics?</a> in the <i>Amazon Web Services HealthOmics User Guide</i>.</p>
  * @public
  */
 export class OmicsClient extends __Client<

clients/client-omics/src/commands/CancelRunCommand.ts

@@ -28,7 +28,7 @@ export interface CancelRunCommandInput extends CancelRunRequest {}
 export interface CancelRunCommandOutput extends __MetadataBearer {}
 
 /**
- * <p>Cancels a run.</p>
+ * <p>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 <code>ListRuns</code> API operation to check that it is no longer listed.</p>
  * @example
  * Use a bare-bones client and the command you need to make an API call.
  * ```javascript

clients/client-omics/src/commands/CreateRunCacheCommand.ts

@@ -28,7 +28,7 @@ export interface CreateRunCacheCommandInput extends CreateRunCacheRequest {}
 export interface CreateRunCacheCommandOutput extends CreateRunCacheResponse, __MetadataBearer {}
 
 /**
- * <p>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).</p> <p>For more information, see <a href="https://docs.aws.amazon.com/omics/latest/dev/workflow-cache-create.html">Creating a run cache</a> in the Amazon Web Services HealthOmics User Guide.</p>
+ * <p>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.</p> <p>For more information, see <a href="https://docs.aws.amazon.com/omics/latest/dev/workflows-call-caching.html">Call caching</a> and <a href="https://docs.aws.amazon.com/omics/latest/dev/workflow-cache-create.html">Creating a run cache</a> in the <i>Amazon Web Services HealthOmics User Guide</i>.</p>
  * @example
  * Use a bare-bones client and the command you need to make an API call.
  * ```javascript

clients/client-omics/src/commands/CreateRunGroupCommand.ts

@@ -28,7 +28,7 @@ export interface CreateRunGroupCommandInput extends CreateRunGroupRequest {}
 export interface CreateRunGroupCommandOutput extends CreateRunGroupResponse, __MetadataBearer {}
 
 /**
- * <p>You can optionally create a run group to limit the compute resources for the runs that you add to the group.</p>
+ * <p>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.</p>
  * @example
  * Use a bare-bones client and the command you need to make an API call.
  * ```javascript

clients/client-omics/src/commands/CreateWorkflowCommand.ts

@@ -28,7 +28,7 @@ export interface CreateWorkflowCommandInput extends CreateWorkflowRequest {}
 export interface CreateWorkflowCommandOutput extends CreateWorkflowResponse, __MetadataBearer {}
 
 /**
- * <p>Creates a private workflow.Private workflows depend on a variety of resources that you create and configure before creating the workflow:</p> <ul> <li> <p> <i>Input data</i>: Input data for the workflow, stored in an S3 bucket or a Amazon Web Services HealthOmics sequence store. </p> </li> <li> <p> <i>Workflow definition files</i>: 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.</p> </li> <li> <p> <i>Parameter template files</i>: Define run parameters using a parameter template file (written in JSON). </p> </li> <li> <p> <i>ECR container images</i>: Create one or more container images for the workflow. Store the images in a private ECR repository.</p> </li> <li> <p>(Optional) <i>Sentieon licenses</i>: Request a Sentieon license if you plan to use Sentieon software in a private workflow.</p> </li> </ul> <p>For more information, see <a href="https://docs.aws.amazon.com/omics/latest/dev/creating-private-workflows.html">Creating or updating a private workflow in Amazon Web Services HealthOmics</a> in the Amazon Web Services HealthOmics User Guide.</p>
+ * <p>Creates a private workflow. Before you create a private workflow, you must create and configure these required resources:</p> <ul> <li> <p> <i>Workflow definition files</i>: Define your workflow in one or more workflow definition files, written in WDL, Nextflow, or CWL. The workflow definition specifies the inputs and outputs for runs that use the workflow. It also includes specifications for the runs and run tasks for your workflow, including compute and memory requirements. The workflow definition file must be in .zip format.</p> </li> <li> <p>(Optional) <i>Parameter template</i>: You can create a parameter template file that defines the run parameters, or Amazon Web Services HealthOmics can generate the parameter template for you.</p> </li> <li> <p> <i>ECR container images</i>: Create one or more container images for the workflow. Store the images in a private ECR repository.</p> </li> <li> <p>(Optional) <i>Sentieon licenses</i>: Request a Sentieon license if using the Sentieon software in a private workflow.</p> </li> </ul> <p>For more information, see <a href="https://docs.aws.amazon.com/omics/latest/dev/creating-private-workflows.html">Creating or updating a private workflow in Amazon Web Services HealthOmics</a> in the <i>Amazon Web Services HealthOmics User Guide</i>.</p>
  * @example
  * Use a bare-bones client and the command you need to make an API call.
  * ```javascript
@@ -55,6 +55,22 @@ export interface CreateWorkflowCommandOutput extends CreateWorkflowResponse, __M
  *   requestId: "STRING_VALUE", // required
  *   accelerators: "STRING_VALUE",
  *   storageType: "STRING_VALUE",
+ *   readmeMarkdown: "STRING_VALUE",
+ *   parameterTemplatePath: "STRING_VALUE",
+ *   readmePath: "STRING_VALUE",
+ *   definitionRepository: { // DefinitionRepository
+ *     connectionArn: "STRING_VALUE", // required
+ *     fullRepositoryId: "STRING_VALUE", // required
+ *     sourceReference: { // SourceReference
+ *       type: "STRING_VALUE", // required
+ *       value: "STRING_VALUE", // required
+ *     },
+ *     excludeFilePatterns: [ // ExcludeFilePatternList
+ *       "STRING_VALUE",
+ *     ],
+ *   },
+ *   workflowBucketOwnerId: "STRING_VALUE",
+ *   readmeUri: "STRING_VALUE",
  * };
  * const command = new CreateWorkflowCommand(input);
  * const response = await client.send(command);

clients/client-omics/src/commands/CreateWorkflowVersionCommand.ts

@@ -28,7 +28,7 @@ export interface CreateWorkflowVersionCommandInput extends CreateWorkflowVersion
 export interface CreateWorkflowVersionCommandOutput extends CreateWorkflowVersionResponse, __MetadataBearer {}
 
 /**
- * <p>Creates a new workflow version for the workflow that you specify with the <code>workflowId</code> parameter.</p> <p>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.</p> <p>Provide a version name that is unique for this workflow. You cannot change the name after HealthOmics creates the version.</p> <note> <p>Don’t include any personally identifiable information (PII) in the version name. Version names appear in the workflow version ARN.</p> </note> <p>For more information, see <a href="https://docs.aws.amazon.com/omics/latest/dev/workflow-versions.html">Workflow versioning in Amazon Web Services HealthOmics</a> in the Amazon Web Services HealthOmics User Guide.</p>
+ * <p>Creates a new workflow version for the workflow that you specify with the <code>workflowId</code> parameter.</p> <p>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.</p> <p>Provide a version name that is unique for this workflow. You cannot change the name after HealthOmics creates the version.</p> <note> <p>Don’t include any personally identifiable information (PII) in the version name. Version names appear in the workflow version ARN.</p> </note> <p>For more information, see <a href="https://docs.aws.amazon.com/omics/latest/dev/workflow-versions.html">Workflow versioning in Amazon Web Services HealthOmics</a> in the <i>Amazon Web Services HealthOmics User Guide</i>.</p>
  * @example
  * Use a bare-bones client and the command you need to make an API call.
  * ```javascript
@@ -57,6 +57,21 @@ export interface CreateWorkflowVersionCommandOutput extends CreateWorkflowVersio
  *     "<keys>": "STRING_VALUE",
  *   },
  *   workflowBucketOwnerId: "STRING_VALUE",
+ *   readmeMarkdown: "STRING_VALUE",
+ *   parameterTemplatePath: "STRING_VALUE",
+ *   readmePath: "STRING_VALUE",
+ *   definitionRepository: { // DefinitionRepository
+ *     connectionArn: "STRING_VALUE", // required
+ *     fullRepositoryId: "STRING_VALUE", // required
+ *     sourceReference: { // SourceReference
+ *       type: "STRING_VALUE", // required
+ *       value: "STRING_VALUE", // required
+ *     },
+ *     excludeFilePatterns: [ // ExcludeFilePatternList
+ *       "STRING_VALUE",
+ *     ],
+ *   },
+ *   readmeUri: "STRING_VALUE",
  * };
  * const command = new CreateWorkflowVersionCommand(input);
  * const response = await client.send(command);

clients/client-omics/src/commands/DeleteRunCacheCommand.ts

@@ -28,7 +28,7 @@ export interface DeleteRunCacheCommandInput extends DeleteRunCacheRequest {}
 export interface DeleteRunCacheCommandOutput extends __MetadataBearer {}
 
 /**
- * <p>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 <code>Delete</code> operations. </p> <p>For more information, see <a href="https://docs.aws.amazon.com/omics/latest/dev/workflow-cache-delete.html">Deleting a run cache</a> in the Amazon Web Services HealthOmics User Guide.</p>
+ * <p>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 <code>Delete</code> operations. </p> <p>For more information, see <a href="https://docs.aws.amazon.com/omics/latest/dev/workflow-cache-delete.html">Deleting a run cache</a> in the <i>Amazon Web Services HealthOmics User Guide</i>.</p>
  * @example
  * Use a bare-bones client and the command you need to make an API call.
  * ```javascript

clients/client-omics/src/commands/DeleteRunCommand.ts

@@ -28,7 +28,7 @@ export interface DeleteRunCommandInput extends DeleteRunRequest {}
 export interface DeleteRunCommandOutput extends __MetadataBearer {}
 
 /**
- * <p>Deletes a workflow run.</p>
+ * <p>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 <code>COMPLETED</code>, <code>FAILED</code>, or <code>CANCELLED</code> 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.</p> <p>To verify that the workflow is deleted:</p> <ul> <li> <p>Use <code>ListRuns</code> to confirm the workflow no longer appears in the list.</p> </li> <li> <p>Use <code>GetRun</code> to verify the workflow cannot be found.</p> </li> </ul>
  * @example
  * Use a bare-bones client and the command you need to make an API call.
  * ```javascript