AWS omics medium security documentation change
Summary
Updated workflow creation steps to add Git repository integration, clarify UI navigation, restructure parameters, and expand storage/parameter configuration options
Security assessment
Added requirement to specify S3 bucket owner's account ID when using external buckets (prevents unauthorized access) and introduced repository connection configuration with explicit region requirements for TLV customers (ensures proper access control). The exclusion patterns help prevent accidental inclusion of sensitive files.
Diff
diff --git a/omics/latest/dev/workflows-version-create.md b/omics/latest/dev/workflows-version-create.md index 7d2df6a74..cce3d3cbf 100644 --- a//omics/latest/dev/workflows-version-create.md +++ b//omics/latest/dev/workflows-version-create.md @@ -42 +42 @@ After you delete a workflow version, HealthOmics lets you reuse the version name -###### To create a workflow +###### Steps to create a workflow @@ -46 +46 @@ After you delete a workflow version, HealthOmics lets you reuse the version name - 2. In the left navigation pane, choose **Private workflows**. + 2. Select the navigation pane (≡) in the top left, and select **Private workflows**. @@ -54 +54 @@ After you delete a workflow version, HealthOmics lets you reuse the version name - * **Version name** \- Enter a name for the workflow version that is unique across the workflow. + 1. **Version name** : Enter a name for the workflow version that is unique across the workflow. @@ -56 +56 @@ After you delete a workflow version, HealthOmics lets you reuse the version name - * **Version description** (optional) - you can use the description field to add notes about this version. + 2. **Version description** (optional): You can use the description field to add notes about this version. @@ -58 +58 @@ After you delete a workflow version, HealthOmics lets you reuse the version name - 6. In the **Workflow definition** panel, provide the following information + 6. In the **Workflow definition** panel, provide the following information: @@ -60 +60 @@ After you delete a workflow version, HealthOmics lets you reuse the version name - * **Workflow language** (optional) - you can select the specification language for the workflow version. Otherwise, HealthOmics determines the language from the workflow definition. + 1. **Workflow language** (optional): Select the specification language for the workflow version. Otherwise, HealthOmics determines the language from the workflow definition. @@ -62 +62 @@ After you delete a workflow version, HealthOmics lets you reuse the version name - * For **Workflow definition source** , choose whether to retrieve the definition folder from an Amazon S3 location or from a local drive. + 2. For **Workflow definition source** , choose to import the definition folder from a Git-based repository, an Amazon S3 location, or from a local drive. @@ -64 +64 @@ After you delete a workflow version, HealthOmics lets you reuse the version name - * If you choose **Select definion folder from S3** : + 1. For **Import from a repository service** : @@ -66 +66,15 @@ After you delete a workflow version, HealthOmics lets you reuse the version name - * Enter the Amazon S3 location that contains the zipped workflow definition folder. +###### Note + +HealthOmics supports public and private repositories for GitHub, GitLab, Bitbucket, GitHub self-managed, GitLab self-managed. + + 1. Choose a **Connection** to connect your AWS resources to the external repository. To create a connection, see [Connect with external code repositories](./setting-up-new.html#setting-up-omics-repository). + +###### Note + +Customers in the TLV region need to create a connection in the IAD (us-east-1) region to create a workflow. + + 2. In **Full repository ID** , enter your repository ID as user-name/repo-name. Verify you have access to the files in this repository. + + 3. In **Source reference** (optional), enter a repository source reference (branch, tag, or commit ID). HealthOmics uses the default branch if no source reference is specified. + + 4. In **Exclude file patterns** , enter the file patterns to exclude specific folders, files, or extensions. This helps manage data size when importing repository files. There is a max of 50 patterns, and the patters must follow the [glob pattern syntax](https://fossil-scm.org/home/doc/tip/www/globs.md). For example: @@ -68 +82 @@ After you delete a workflow version, HealthOmics lets you reuse the version name - * If your account doesn't own the S3 bucket, enter the bucket owner's AWS account ID in **S3 bucket owner's account ID**. This information is required so that HealthOmics can verify the bucket ownership. + 1. `tests/` @@ -70 +84 @@ After you delete a workflow version, HealthOmics lets you reuse the version name - * If you choose **Select definion folder from a local source** , enter the local drive location of the zipped workflow definition folder. + 2. `*.jpeg` @@ -72 +86 @@ After you delete a workflow version, HealthOmics lets you reuse the version name - * **Main workflow definition file path** (optional) - enter the file path from the zipped workflow definition folder to the main file. This parameter is not required if there is only one file in the workflow definition folder, or if the main file is named "main". + 3. `large_data.zip` @@ -74 +88 @@ After you delete a workflow version, HealthOmics lets you reuse the version name - 7. In the **Default run storage configuration** panel, provide the default run storage type and capacity for runs that use this workflow version: + 2. For **Select definition folder from S3** : @@ -76 +90 @@ After you delete a workflow version, HealthOmics lets you reuse the version name - * **Run storage type** (optional) - choose whether to use static or dynamic storage as the default for the temporary run storage. The default is dynamic storage. + 1. Enter the Amazon S3 location that contains the zipped workflow definition folder. The Amazon S3 bucket must be in the same region as the workflow. @@ -78 +92 @@ After you delete a workflow version, HealthOmics lets you reuse the version name - * **Run storage capacity** (optional) - If you choose static run storage type, you can enter 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 1200 GiB. + 2. If your account doesn't own the Amazon S3 bucket, enter the bucket owner's AWS account ID in the **S3 bucket owner's account ID**. This information is required so that HealthOmics can verify the bucket ownership. @@ -80 +94 @@ After you delete a workflow version, HealthOmics lets you reuse the version name -You can override these default values when you start a run. + 3. For **Select definition folder from a local source** : @@ -82 +96,11 @@ You can override these default values when you start a run. - 8. **Tags** (optional) - you can associate up to 50 tags with this workflow version. + 1. Enter the local drive location of the zipped workflow definition folder. + + 3. **Main workflow definition file path** (optional): Enter the file path from the zipped workflow definition folder or repository to the `main` file. This parameter is not required if there is only one file in the workflow definition folder, or if the main file is named "main". + + 7. In the **Default run storage configuration** panel, provide the default run storage type and capacity for runs that use this workflow: + + 1. **Run storage type** : Choose whether to use static or dynamic storage as the default for the temporary run storage. The default is static storage. + + 2. **Run storage capacity** (optional): For static run storage type, you can enter the default amount of run storage required for this workflow. The default value for this parameter is 1200 GiB. You can override these default values when you start a run. + + 8. **Tags** (optional): You can associate up to 50 tags with this workflow version. @@ -86 +110,9 @@ You can override these default values when you start a run. - 10. On the **Add workflow parameters** page, provide the workflow parameters. You can upload a JSON file that specifies the parameters or manually enter your workflow parameters. If you are using CWL, you can choose **Add from CWL workflow definition file**. + 10. On the **Add workflow parameters** (optional) page, select the **Parameter source** : + + 1. For **Parse from workflow definition file** , HealthOmics will automatically parse the workflow parameters from the workflow definition file. + + 2. For **Provide parameter template from Git repository** , use the path to the parameter template file from your repository. + + 3. For **Select JSON file from local source** , upload a JSON file from a local source that specifies the parameters. + + 4. For **Manually enter workflow parameters** , manually enter parameter names and descriptions. @@ -88 +120 @@ You can override these default values when you start a run. -In **Parameter preview** , you can review or change the parameters for this workflow version. If you restore the JSON file, you lose any local changes that you made. + 11. In the **Parameter preview** panel, you can review or change the parameters for this workflow version. If you restore the JSON file, you lose any local changes that you made. @@ -90 +122 @@ In **Parameter preview** , you can review or change the parameters for this work - 11. Choose **Next**. + 12. Choose **Next**. @@ -92 +124 @@ In **Parameter preview** , you can review or change the parameters for this work - 12. Review the version configuration, then choose **Create version**. + 13. Review the version configuration, then choose **Create version**.