AWS omics documentation change
Summary
Restructured documentation to focus on workflow lifecycle management (create/update/delete), removed detailed implementation steps for console/CLI/SDK, added workflow versioning guidance, and converted procedural content into topic links
Security assessment
The changes are organizational/structural improvements rather than security-related. No security vulnerabilities, mitigations, or security features are mentioned. The versioning guidance relates to general maintenance rather than security hardening
Diff
diff --git a/omics/latest/dev/creating-private-workflows.md b/omics/latest/dev/creating-private-workflows.md index 0e76d8dbd..3307126ac 100644 --- a//omics/latest/dev/creating-private-workflows.md +++ b//omics/latest/dev/creating-private-workflows.md @@ -5,3 +5 @@ -Creating a workflow using the console Creating a workflow using the CLICreating a workflow using an SDKOptional parameters to use when creating a workflow Referencing genome files from a workflow definitionVerifying the status of a workflow - -# Creating a HealthOmics private workflow +# Creating or updating a workflow @@ -20,65 +18 @@ If your workflow definition file is larger than 4 MiB (zipped), upload it to an -###### Topics - - * Creating a workflow using the console - - * Creating a workflow using the CLI - - * Creating a workflow using an SDK - - * Optional parameters to use when creating a workflow - - * Referencing genome files from a workflow definition - - * Verifying the status of a workflow - - - - -## Creating a workflow using the console - -###### To create a workflow - - 1. Open the HealthOmics console [https://console.aws.amazon.com/omics/](https://console.aws.amazon.com/omics/). - - 2. In the left navigation pane, choose **Private workflows**. - - 3. On the **Private workflows** page, choose **Create workflow**. - - 4. On the **Create workflow** page, provide the following information - - * **Workflow name** \- A distinctive name for this workflow. - - * **Description** (optional) - A description of this workflow. - - * **Default run storage capacity** (optional) - The default amount of run storage required for this workflow. You can override this default when you start a workflow run. The default value for this parameter is 1.2 TB. - - * Under **Workflow definition** , if you choose **Select definion folder from S3** , enter the Amazon S3 location that contains the zipped workflow definition folder. - - * If you choose **Select definion folder from a local source** , enter the location of the zipped workflow definition folder. - - * For **Workflow language** , select the specification language of the workflow. - - * **Tags** (optional) - Provide up to 50 tags for this workflow. - - 5. Choose **Next**. - - 6. On the **Add workflow parameters** page, provide the workflow parameters. You can either upload a JSON file that specifies the parameters or manually enter your workflow parameters. - - 7. Choose **Next**. - - 8. Review the workflow configuration, then choose **Create workflow**. - - - - -## Creating a workflow using the CLI - -After you define your workflow and the parameters, you can create a workflow using the CLI as shown. - - - aws omics create-workflow - --name my_workflow - --definition-zip fileb://my-definition.zip \ - --parameter-template file://my-parameter-template.json - -If your workflow definition file located in an Amazon S3 folder, enter the location using the `--definition-uri` parameter instead of `--definition-zip`. For more information, see [CreateWorkflow](https://docs.aws.amazon.com/omics/latest/api/API_CreateWorkflow.html) in the AWS HealthOmics API Reference. +After you create a workflow, you can change only a few of the configuration values. To change other information in the workflow, you can either create a new workflow or a new version of the workflow. @@ -86 +20 @@ If your workflow definition file located in an Amazon S3 folder, enter the locat -You receive the following response to the `create-workflow` request. +You can use workflow versioning to organize and structure you workflows. Versions also help you to manage the introduction of iterative workflow updates. For more information about versions, see [Create a workflow version](./workflows-version-create.html). @@ -87,0 +22 @@ You receive the following response to the `create-workflow` request. +###### Topics @@ -89,90 +24 @@ You receive the following response to the `create-workflow` request. - { - "arn": "arn:aws:omics:us-west-2:....", - "id": "1234567", - "status": "CREATING", - "tags": { - "resourceArn": "arn:aws:omics:us-west-2:...." - } - } - -## Creating a workflow using an SDK - -You can create a workflow using one of the SDKs. - -The following example shows how to create a workflow using the Python SDK - - - import boto3 - - omics = boto3.client('omics') - - with open('definition.zip', 'rb') as f: - definition = f.read() - - response = omics.create_workflow( - name='my_workflow', - definitionZip=definition, - parameterTemplate={ ... } - ) - -## Optional parameters to use when creating a workflow - -You can specify one or more optional parameters when you create a workflow. For more information, see [CreateWorkflow](https://docs.aws.amazon.com/omics/latest/api/API_CreateWorkflow.html) in the AWS HealthOmics API Reference. - -If you are including multiple workflow definition files, use the `--main` parameter to specify which file is the main definition file for your workflow. - -If you uploaded your workflow definition file to an Amazon S3 folder, specify the location using the `--definition-uri` parameter, as shown in the following example. - - - aws omics create-workflow - --name Test --main multi_workflow/workflow2.wdl - --definition-zip fileb://definition.zip - --parameter-template file://params_sample_description.json - -Use the accelerators parameter to create a workflow that runs on an accelerated-compute instance. The following example shows how to use the `--accelerators` parameter. - - - aws omics create-workflow --name workflow name \ - --definition-uri s3://amzn-s3-demo-bucket1/GPUWorkflow.zip \ - --accelerators GPU - -## Referencing genome files from a workflow definition - -An HealthOmics reference store object can be referred to with a URI like the following. Use your own ``account ID``, ``reference store ID``, and ``reference ID`` where indicated. - - - omics://account ID.storage.us-west-2.amazonaws.com/reference store id/reference/id - -Some workflows will require both the `SOURCE` and `INDEX` files for the reference genome. The previous URI is the default short form and will default to the SOURCE file. In order to specify either file, you can use the long URI form, as follows. - - - omics://account ID.storage.us-west-2.amazonaws.com/reference store id/reference/id/source - omics://account ID.storage.us-west-2.amazonaws.com/reference store id/reference/id/index - -Using a sequence read set would have a similar pattern, as shown. - - - aws omics create-workflow \ - --name workflow name \ - --main sample workflow.wdl \ - --definition-uri omics://account ID.storage.us-west-2.amazonaws.com/sequence_store_id/readSet/id \ - --parameter-template file://parameters_sample_description.json - -Some read sets, such as those based on FASTQ, can contain paired reads. In the following examples, they’re referred to as SOURCE1 and SOURCE2. Formats such as BAM and CRAM will only have a SOURCE1 file. Some read sets will contain INDEX files such as `bai` or `crai` files. The preceding URI is the default short form and will default to the SOURCE1 file. To specify the exact file or index, you can use the long URI form, as follows. - - - omics://123456789012.storage.us-west-2.amazonaws.com/<sequence_store_id>/readSet/<id>/source1 - omics://123456789012.storage.us-west-2.amazonaws.com/<sequence_store_id>/readSet/<id>/source2 - omics://123456789012.storage.us-west-2.amazonaws.com/<sequence_store_id>/readSet/<id>/index - -The following is an example of an input JSON file that uses two Omics Storage URIs. - - - { - "input_fasta": "omics://123456789012.storage.us-west-2.amazonaws.com/<reference_store_id>/reference/<id>", - "input_cram": "omics://123456789012.storage.us-west-2.amazonaws.com/<sequence_store_id>/readSet/<id>" - } - -Reference the input JSON file in the AWS CLI by adding `--inputs file://<input_file.json>` to your **start-run** request. - -## Verifying the status of a workflow + * [Create a private workflow](./create-private-workflow.html) @@ -180 +26 @@ Reference the input JSON file in the AWS CLI by adding `--inputs file://<input_f -After you create your workflow, you can verify the status and view other details of the workflow using **get-workflow** , as shown. + * [Update a private workflow](./update-private-workflow.html) @@ -181,0 +28 @@ After you create your workflow, you can verify the status and view other details + * [Delete a private workflow](./delete-private-workflow.html) @@ -183 +30 @@ After you create your workflow, you can verify the status and view other details - aws omics get-workflow --id 1234567 + * [Verify the workflow status](./using-get-workflow.html) @@ -185 +32 @@ After you create your workflow, you can verify the status and view other details -The response gives you your workflow details, including the status, as shown. + * [Referencing genome files from a workflow definition](./create-ref-files.html) @@ -188,8 +34,0 @@ The response gives you your workflow details, including the status, as shown. - { - "arn": "arn:aws:omics:us-west-2:....", - "id": "1234567", - "status": "ACTIVE", - "type": "PRIVATE", - "name": "workflow_name" - "creationTime": "2022-07-06T00:27:05.542459" - } @@ -197 +35,0 @@ The response gives you your workflow details, including the status, as shown. -Before a run can be started, the status must be listed as `ACTIVE`. @@ -207 +45 @@ Workflow linters -Starting runs +Create a workflow