Update plugins documentation

docs/gradle-plugin.md

@@ -65,25 +65,21 @@ To run unit tests:
 
 ## Packaging, uploading, and publishing a plugin
 
-The Gradle plugin for Nextflow plugins simplifies publishing your plugin.
+The Gradle plugin for Nextflow plugins simplifies publishing your plugin to the Nextflow Plugin Registry.
 
-To package, upload, and publish your plugin:
+:::{note}
+The Nextflow Plugin Registry is currently available as private beta technology. Contact [info@nextflow.io](mailto:info@nextflow.io) to learn how to get access.
+:::
 
-1. Fork the [Nextfow plugins index repository](https://github.com/nextflow-io/plugins).
-2. In the plugin root directory, open `build.gradle` and ensure that:
-    * `github.repository` matches the plugin repository.
-    * `github.indexUrl` matches your fork of the plugins index repository.
-3. Create a file named `$HOME/.gradle/gradle.properties` and add the following:
+To package, upload, and publish your plugin to the Nextflow Plugin Registry:
+
+1. Create a file named `$HOME/.gradle/gradle.properties`, where `$HOME` is your home directory.
+2. Add the following properties:
 
     ```bash
-    github_username=<GITHUB_USERNAME>
-    github_access_token=<GITHUB_ACCESS_TOKEN>
-    github_commit_email=<GITHUB_EMAIL>
+    pluginRegistry.accessToken=<REGISTRY_ACCESS_TOKEN>
     ```
 
-    Replace the following:
-    * `GITHUB_USERNAME`: your GitHub username granting access to the plugin repository.
-    * `GITHUB_ACCESS_TOKEN`: your GitHub access token with permission to upload and commit changes to the plugin repository.
-    * `GITHUB_EMAIL`: your email address associated with your GitHub account.
-4. Run `make release`.
-5. Create a pull request against the [Nextfow plugins index repository](https://github.com/nextflow-io/plugins) from your fork.
+    Replace <REGISTRY_ACCESS_TOKEN> with your plugin registry access token.
+
+3. Run `make release`.

docs/migrating-gradle-plugin.md

@@ -15,10 +15,14 @@ The Gradle plugin for Nextflow plugins simplifies and standardizes the developme
 
 The Gradle plugin is versioned and published to the [Gradle Plugin Portal](https://plugins.gradle.org/), allowing developers to manage it like any other dependency. As the plugin ecosystem evolves, this Gradle plugin will enable easier maintenance and adoption of ongoing improvements to the Nextflow plugin framework.
 
-### Nextflow plugin registry
+### Nextflow Plugin Registry
 
 The Nextflow plugin registry is a centralized repository of assembled plugins. It hosts an index of plugin metadata that supports plugin discovery, accessibility, and version tracking. The registry is integrated with the Nextflow runtime. Nextflow will automatically locate and download configured plugins.
 
+:::{note}
+The Nextflow Plugin Registry is currently available as private beta technology. Contact [info@nextflow.io](mailto:info@nextflow.io) to learn how to get access.
+:::
+
 ## Impact on users and developers
 
 The impact of the Gradle plugin for Nextflow plugins differs for plugin users and developers.
@@ -57,7 +61,7 @@ To migrate an existing Nextflow plugin:
     ```groovy
     // Plugins
     plugins {
-        id 'io.nextflow.nextflow-plugin' version '0.0.1-alpha3'
+        id 'io.nextflow.nextflow-plugin' version '0.0.1-alpha4'
     }
 
     // Dependencies (optional)
@@ -79,13 +83,10 @@ To migrate an existing Nextflow plugin:
             '<EXTENSION_POINT>'
         ]
 
-        publishing {
-            github {
-                repository = '<GITHUB_REPOSITORY>'
-                userName = project.findProperty('github_username')
-                authToken = project.findProperty('github_access_token')
-                email = project.findProperty('github_commit_email')
-                indexUrl = '<GITHUB_INDEX_URL>'
+    publishing {
+            registry {
+                url = 'https://nf-plugins-registry.dev-tower.net/api'
+                authToken = project.findProperty('pluginRegistry.accessToken')
             }
         }
     }
@@ -99,8 +100,6 @@ To migrate an existing Nextflow plugin:
     - `PROVIDER`: Your name or organization—for example, `acme`.
     - `CLASS_NAME`: Your plugin class name—for example, `acme.plugin.MyPlugin`.
     - `EXTENSION_POINT`: Your extension point identifiers that the plugin will implement or expose—for example, `acme.plugin.MyFactory`.
-    - `GITHUB_REPOSITORY`: Your GitHub plugin repository name—for example, `nextflow-io/nf-plugin-template`.
-    - `GITHUB_INDEX_URL`: The URL of your fork of the plugins index repository—for example, [`https://github.com/nextflow-io/plugins/blob/main/plugins.json`](https://github.com/nextflow-io/plugins/blob/main/plugins.json).
 
 5. Replace the contents of `Makefile` with the following:
 

docs/plugins/developing-plugins.md

@@ -56,7 +56,7 @@ The Gradle plugin is versioned and published to the [Gradle Plugin Portal](https
 
 ```nextflow
 plugins {
-    id 'io.nextflow.nextflow-plugin' version '0.0.1-alpha3'
+    id 'io.nextflow.nextflow-plugin' version '0.0.1-alpha4'
 }
 ```
 

docs/plugins/example-nf-hello.md

@@ -54,7 +54,7 @@ It also includes several classes that demonstrate different plugin functionality
 The `nf-hello` plugin can be configured via nextflow configuration files or at runtime. For example:
 
 ```bash
-nextflow run hello -plugins nf-hello@0.5.0,nf-amazon@2.9.0
+nextflow run hello -plugins nf-hello@0.5.0
 ```
 
 See the [nf-hello plugin repository](https://github.com/nextflow-io/nf-hello/tree/gradle-plugin-example) for the plugin source code.