Update local_installation documentation and mark jobsNamespace override as REQUIRED

Author: nss10

.secrets.baseline

@@ -151,7 +151,7 @@
         "filename": "docs/local_installation.md",
         "hashed_secret": "08d2e98e6754af941484848930ccbaddfefe13d6",
         "is_verified": false,
-        "line_number": 88
+        "line_number": 90
       }
     ],
     "docs/s3.md": [
@@ -209,5 +209,5 @@
       }
     ]
   },
-  "generated_at": "2026-01-09T21:30:34Z"
+  "generated_at": "2026-02-03T17:56:09Z"
 }

docs/gen3-deployment.md

@@ -17,11 +17,8 @@ gen3-workflow:
 
 ## 2. Configure Gen3Workflow
 
-You can customize Gen3Workflow by overriding values under `gen3WorkflowConfig` in your `values.yaml`.
-
-The default configuration is available here:
-[gen3-workflow/values.yaml#L308](https://github.com/uc-cdis/gen3-helm/blob/master/helm/gen3-workflow/values.yaml#L308)
-(See `.Values.gen3WorkflowConfig`)
+* You can customize Gen3Workflow by overriding values under `gen3WorkflowConfig` in your `values.yaml`.
+* The default configuration is available here: [gen3-workflow/values.yaml#L308](https://github.com/uc-cdis/gen3-helm/blob/master/helm/gen3-workflow/values.yaml#L308) (See `.Values.gen3WorkflowConfig`)
 
 ---
 
@@ -59,10 +56,8 @@ Gen3Workflow requires specific IAM roles and policies.
 
 ## 5. Authorization Setup
 
-Update your `user.yaml` as described in the authorization guide:
-* [Authorization Documentation](authorization.md)
-
-After updating, run the `usersync` job to apply the changes.
+* Update your `user.yaml` as described in the authorization guide: **[Authorization Documentation](authorization.md)**
+* After updating, run the `usersync` job to apply the changes.
 
 ---
 
@@ -81,8 +76,19 @@ gen3WorkflowConfig:
             jobsNamespace: <jobs-namespace>
 ```
 
-**Recommendation:**
-Use a naming convention such as: `workflow-pods-<release-namespace>`
+### **Requirement: JobsNamespace Naming Convention**
+
+Funnel supports any Kubernetes-compatible value for `JobsNamespace`. However, when using Funnel together with **Gen3 Workflow**, a specific naming convention is required.
+
+> **Required:**
+> Users **must** set `JobsNamespace` to:
+>
+> ```
+> workflow-pods-<release-namespace>
+> ```
+
+This naming convention is required to ensure correct integration and expected behavior between Gen3 Workflow and Funnel. Using a different value may result in deployment issues or unexpected runtime behavior.
+
 
 Example:
 
@@ -93,16 +99,16 @@ gen3WorkflowConfig:
             jobsNamespace: workflow-pods-qa-midrc
 ```
 
-### 7. Helm Chart architecture
-* More information regarding how the helm chart is designed can be found in this document -- [WIP-Placeholder link](#placeholder_link)
+## 7. Helm Chart Architecture
 
----
-
-## Documentation WIP
+* For more details on how the Helm chart is designed, refer to the [Helm Chart Architecture](architecture.md#helm-chart-architecture) document.
 
-9. Follow [these steps](local_installation.md#run-nextflow-workflows-with-gen3workflow) to test the deployment.
+## 8. Nextflow tests
+* Follow the steps in [Run Nextflow workflows with Gen3Workflow](local_installation.md#run-nextflow-workflows-with-gen3workflow) to test the deployment using Nextflow workflows.
+* When deploying Gen3 Workflow to a Gen3 instance, ensure **Gen3Workflow URL** is set to your commons' endpoint URL.
+---
 
-## Automation notes
+## 9. Automation notes
 
 Some manual steps are currently necessary to deploy Gen3Workflow to a new Gen3 instance.
 

docs/local_installation.md

@@ -67,6 +67,8 @@ python run.py
 
 Try out the API at <http://localhost:8080/_status> or <http://localhost:8080/docs> (you might have to set `DOCS_URL_PREFIX` to `""` in your configuration file for the docs endpoint to work).
 
+>Note: Although the gen3-workflow service can run as a standalone component, a complete end-to-end experience with Funnel and the Funnel plugin requires interaction with the Fence service. While support for this workflow is planned for future releases, it is not currently supported out of the box.
+
 ## Run Nextflow workflows with Gen3Workflow
 
 - Hit the `/storage/info` endpoint to get your working directory
@@ -113,7 +115,7 @@ gen3 run nextflow run hello
 
 ## AWS access
 
-For full functionality, the Gen3Workflow service requires access to perform a number of operations in AWS. The full policy can be found [here](https://github.com/uc-cdis/cloud-automation/blob/master/gen3/bin/kube-setup-gen3-workflow.sh).
+For full functionality, the Gen3Workflow service requires access to perform a number of operations in AWS. The full policy can be found here -- [gen3-workflow/templates/crossplane.yaml](https://github.com/uc-cdis/gen3-helm/blob/master/helm/gen3-workflow/templates/crossplane.yaml)
 
 ## Quickstart with Helm
 
@@ -168,5 +170,5 @@ You can also store your images in a local registry. Kind and Minikube are popula
 - https://minikube.sigs.k8s.io/docs/handbook/registry/#enabling-insecure-registries
 
 Dependencies:
-Gen3Workflow relies on Arborist to run. Please view the [Arborist Quick Start Guide](https://github.com/uc-cdis/arborist) for more information.
-Gen3Workflow also relies on [Funnel](https://ohsu-comp-bio.github.io/funnel) with [Funnel-gen3-plugin](https://github.com/uc-cdis/funnel-gen3-plugin) and [Fence]((https://github.com/uc-cdis/fence))
+* Gen3Workflow relies on Arborist to run. Please view the [Arborist Quick Start Guide](https://github.com/uc-cdis/arborist) for more information.
+* Gen3Workflow also relies on [Funnel](https://ohsu-comp-bio.github.io/funnel) with [Funnel-gen3-plugin](https://github.com/uc-cdis/funnel-gen3-plugin) and [Fence]((https://github.com/uc-cdis/fence))