AWS omics documentation change

Service: omics · 2025-11-13 · Documentation low

File: omics/latest/dev/create-private-workflow.md

Summary

Added documentation for Git-based workflow definitions and README file specifications including repository connections, exclusion patterns, and parameter examples

Security assessment

While the changes involve secure repository connections (connectionArn), they describe standard feature usage rather than addressing security vulnerabilities or introducing new security controls

Diff

diff --git a/omics/latest/dev/create-private-workflow.md b/omics/latest/dev/create-private-workflow.md
index 3f127432e..d57b1c4bc 100644
--- a//omics/latest/dev/create-private-workflow.md
+++ b//omics/latest/dev/create-private-workflow.md
@@ -214,0 +215,4 @@ You can specify any of the optional parameters when you create a workflow. For s
+  * Use the workflow definition from a Git-based repository
+
+  * Specify a Readme file
+
@@ -236,0 +241,82 @@ If your workflow definition file is located in an Amazon S3 folder, specify the
+#### Use the workflow definition from a Git-based repository
+
+To use the workflow definition from a supported Git-based repository, use the `definition-repository` parameter in your request. Don’t provide any other `definition` parameter, as a request fails if it includes more than one input source.
+
+The `definition-respository` parameter contains the following fields:
+
+  * **connectionArn** – ARN of the Code Connection that connects your AWS resources to the external repository.
+
+  * **fullRepositoryId** – Enter the repository ID as `owner-name/repo-name`. Verify you have access to the files in this repository.
+
+  * **sourceReference** (Optional) – Enter a repository reference type (BRANCH, TAG, or COMMIT) and a value.
+
+HealthOmics uses the latest commit on the default branch if you don't specify a source reference.
+
+  * **excludeFilePatterns** (Optional) – Enter the file patterns to exclude specific folders, files, or extensions. This helps manage data size when importing repository files. Provide a maximum of 50 patterns. the patterns must follow the [ glob pattern syntax](https://fossil-scm.org/home/doc/tip/www/globs.md). For example:
+
+    * `tests/`
+
+    * `*.jpeg`
+
+    * `large_data.zip`
+
+
+
+
+When you specify the workflow definition from a Git-based repository, use `parameter-template-path` to specify the parameter template file. If you don’t provide this parameter, HealthOmics creates the workflow without a parameter template.
+
+The following example shows the parameters related to content from a Git-based private repository: 
+    
+    
+    aws omics create-workflow \
+        --name custom-variant \
+        --description "Custom variant calling pipeline" \
+        --engine "WDL" \
+        --definition-repository '{
+                "connectionArn": "arn:aws:codeconnections:us-east-1:123456789012:connection/abcd1234-5678-90ab-cdef-1234567890ab",
+                "fullRepositoryId": "myorg/my-genomics-workflows",
+                "sourceReference": {
+                    "type": "BRANCH",            
+                    "value": "main"        
+                },        
+                "excludeFilePatterns": ["tests/**", "*.log"]   
+          }' \
+        --main "workflows/variant-calling/main.wdl" \
+        --parameter-template-path "parameters/variant-calling-params.json" \
+        --readme-path "docs/variant-calling-README.md" \
+        --storage-type "DYNAMIC" \       
+
+For more examples, see the blog post [ How To Create an AWS HealthOmics Workflows from Content in Git](https://repost.aws/articles/ARCEN7AjhaRSmteczRoc_QsA/how-to-create-an-aws-healthomics-workflows-from-content-in-git).
+
+#### Specify a Readme file
+
+You can specify the README file location using one of the following parameters:
+
+  * **readme-markdown** – String input or a file on your local machine. 
+
+  * **readme-uri** – The URI of a file stored on S3. 
+
+  * **readme-path** – The path to the README file in the repository. 
+
+
+
+
+Use readme-path only in conjunction with **definition-respository**. If you don’t specify any README parameter, HealthOmics imports the root level README.md file in the repository (if it exists).
+
+The following examples show how specify the README file location using readme-path and readme-uri.
+    
+    
+    # Using README from repository
+    aws omics create-workflow \
+        --name "documented-workflow" \
+        --definition-repository '...' \
+        --readme-path "docs/workflow-guide.md"
+    
+    # Using README from S3
+    aws omics create-workflow \
+        --name "s3-readme-workflow" \
+        --definition-repository '...' \
+        --readme-uri "s3://my-bucket/workflow-docs/readme.md"
+
+For more information, see [HealthOmics Workflow README files](./workflows-readme.html).
+
@@ -344 +430 @@ To use the Amazon Web Services Documentation, Javascript must be enabled. Please
-Creating or updating a workflow
+Workflow operations