Migrating to the Nextflow plugin registry

The Nextflow plugin ecosystem is evolving to support a more robust and user-friendly experience by simplifying the development, publishing, and discovery of Nextflow plugins. This page introduces the Nextflow plugin registry, the Nextflow Gradle plugin, and how to migrate to them.

Note

The Nextflow plugin registry and Gradle plugin are currently available as a private beta. Plugin developers are encouraged to contact info@nextflow.io for more information about accessing the registry.

Overview

Nextflow plugin registry

The Nextflow plugin registry is a central repository for Nextflow plugins. It hosts an index of plugin metadata that supports plugin discovery, accessibility, and version tracking. Nextflow 25.04 and later can use the plugin registry as a drop-in replacement for the legacy plugin index hosted on GitHub.

Nextflow Gradle plugin

The Nextflow Gradle plugin simplifies the development of Nextflow plugins. It provides default configuration required for Nextflow integration, as well as custom Gradle tasks for building, testing, and publishing plugins.

The Gradle plugin is versioned and published to the Gradle Plugin Portal, allowing developers to manage it like any other dependency. As the plugin ecosystem evolves, the Gradle plugin will enable easier maintenance and adoption of ongoing improvements to the Nextflow plugin framework.

Timeline

The legacy plugin index will be deprecated in favor of the Nextflow plugin registry.

Note

The following timeline is tentative and subject to modification.

Nextflow 25.04

The Nextflow plugin registry is available as a private beta. Nextflow 25.04 can use the Nextflow plugin registry as an opt-in feature. The Nextflow plugin registry will be automatically kept up-to-date with the legacy plugin index.

During this time, plugin developers are encouraged to experiment with the Gradle plugin and plugin registry.

Nextflow 25.10

The Nextflow plugin registry will be generally available. Nextflow 25.10 will use the plugin registry by default. The legacy plugin index will be closed to new pull requests.

Developers will be required to publish to the Nextflow plugin registry. To ensure continued support for older versions of Nextflow, the legacy plugin index will be automatically kept up-to-date with the Nextflow plugin registry.

Nextflow 26.04

Nextflow 26.04 will only be able to use the Nextflow plugin registry.

At some point in the future, the legacy plugin index will be frozen – it will no longer receives updates from the Nextflow plugin registry. To ensure continued support for older versions of Nextflow, the legacy plugin index will remain available indefinitely.

Impact on plugin users

No immediate actions are required for plugin users. The plugin configuration has not changed.

Impact on plugin developers

Plugin developers will need to update their plugin to publish to the Nextflow plugin registry instead of the legacy plugin index. The easiest way to do this is to migrate to the Nextflow Gradle plugin, which simplifies the development process and supports publishing to the plugin registry from the command line.

Migrating to the Nextflow Gradle plugin

To migrate an existing Nextflow plugin:

Remove the following files and folders:
- buildSrc/
- launch.sh
- plugins/build.gradle
If your plugin has a plugins directory, move the src directory to the project root.

Note

Plugin sources should be in src/main/groovy or src/main/java.
Replace the contents of settings.gradle with the following:
```
rootProject.name = '<PLUGIN_NAME>'
```
Replace PLUGIN_NAME with your plugin name.

In the project root, create a new build.gradle file with the following configuration:

// Plugins
plugins {
    id 'io.nextflow.nextflow-plugin' version '0.0.1-alpha4'
}

// Dependencies (optional)
dependencies {
    <DEPENDENCY>
}

// Plugin version
version = '<PLUGIN_VERSION>'

nextflowPlugin {
    // Minimum Nextflow version
    nextflowVersion = '<MINIMUM_NEXTFLOW_VERSION>'

    // Plugin metadata
    provider = '<PROVIDER>'
    className = '<CLASS_NAME>'
    extensionPoints = [
        '<EXTENSION_POINT>'
    ]

    publishing {
        registry {
            authToken = project.findProperty('pluginRegistry.accessToken')
        }
    }
}

Replace the following:

DEPENDENCY: (Optional) Your plugins dependency libraries—for example, commons-io:commons-io:2.18.0.
PLUGIN_VERSION: Your plugin version—for example, 0.5.0.
MINIMUM_NEXTFLOW_VERSION: The minimum Nextflow version required to run your plugin—for example, 25.04.0.
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.

Replace the contents of Makefile with the following:

# Build the plugin
assemble:
    ./gradlew assemble

clean:
    rm -rf .nextflow*
    rm -rf work
    rm -rf build
    ./gradlew clean

# Run plugin unit tests
test:
    ./gradlew test

# Install the plugin into local nextflow plugins dir
install:
    ./gradlew install

# Publish the plugin
release:
    ./gradlew releasePlugin

Update README.md with information about the structure of your plugin.
In the plugin root directory, run make assemble.

Alternatively, use the nextflow plugin create command to re-create your plugin with the plugin template and add your existing plugin code. See Nextflow plugin template for more information about the plugin template.

Publishing to the Nextflow plugin registry

The Nextflow Gradle plugin supports publishing plugins from the command line. See Publishing a plugin for more information.

Once you migrate to the Gradle plugin, you will no longer be able to publish to the legacy plugin index. See the transition timeline for more information.