This directory should contain plugin subprojects for Nextflow.

The build.gradle defines the main actions for each plugin.

The plugin subproject defines its own build.gradle and setup the required dependencies.

Minimal dependencies shown below:

dependencies {
    compileOnly project(':nextflow')
    compileOnly 'org.slf4j:slf4j-api:1.7.10'
    compileOnly 'org.pf4j:pf4j:3.4.1'

    testImplementation project(':nextflow')
    testImplementation "org.codehaus.groovy:groovy:3.0.5"
    testImplementation "org.codehaus.groovy:groovy-nio:3.0.5"
}

Each plugin subproject directory name has to begin with the prefix nf- and must include a file named src/resources/META-INF/MANIFEST.MF which contains the plugin metadata. The manifest content looks like the following:

Manifest-Version: 1.0
Plugin-Class: the.plugin.ClassName
Plugin-Id: the-plugin-id
Plugin-Provider: Some Provider Name
Plugin-Version: 0.0.0

• NXF_PLUGINS_MODE: Define the plugin system execution mode, either prod for production or dev for development (see below for details).
• NXF_PLUGINS_DIR: the path where the plugins archives are stored/loaded. Default is $NXF_HOME/plugins for production mode and $PWD/plugins for dev mode.
• NXF_PLUGINS_DEFAULT: Whenever use the default plugins when no plugin is specified in the config file.
• `NXF_PLUGINS_DEV: Comma separate separated list of development plugins root directories

When running in development the plugin system uses the DevPluginClasspath to load plugins classes from each plugin project build path e.g. $PWD/plugins/nf-amazon/build/classes and $PWD/plugins/nf-amazon/build/target/libs (for deps libraries).

The plugins meta-info are published via a GitHub repository at https://github.com/nextflow-io/plugins and accessible through the URL https://raw.githubusercontent.com/nextflow-io/plugins/main/plugins.json.

The repository index has the following structure:

[
  {
    "id": "nf-amazon",
    "releases": [
      {
        "version": "0.2.0",
        "url": "https://github.com/nextflow-io/nf-amazon/releases/download/0.2.0/nf-amazon-0.2.0.zip",
        "date": "2020-10-12T10:05:44.28+02:00",
        "sha512sum": "9e9e33695c1a7c051271..."
      }
    ]
  },
  :
]

A plugin is a ZIP file holding either the plugin classes and the required dependencies JAR file.

Nextflow core plugins are stored in the corresponding GitHub project release page. However, this is not a strict requirement, it has been chosen to simplify the build deployment process and provide a more consistent download experience keeping all of them with the GitHub nextflow-io organization.

Plugins need to be declared in the nextflow.config file using the plugins scope, eg.

plugins {
    id 'nf-amazon@0.2.0'
}

If the plugins is not locally available Nextflow check in the repository index for the download URL, download the ZIP in a temporary file, unzip and store the final plugin in the directory specified by the variable NXF_PLUGINS_DIR (default: $NXF_HOME/plugins).

Finally, since each Nextflow run can have a different set of plugins (and version) requirement, each Nextflow instance keep local plugins directory root in directory $PWD/.nextflow/plr/<unique id> symlinking the exact list of plugins directory required for the current Nextflow instance.

If no plugins are specified in the nextflow.config file, Nextflow default plugins are automatically added. The default plugins list is defined in the Nextflow resources file included in the distribution runtime ./modules/nextflow/src/main/resources/META-INF/plugins-info.txt.

To disable the use of defualt plugins set the following variable NXF_PLUGINS_DEFAULT=false.

Creates the plugin the zip file and the json meta file in the subproject build/libs directory.

» ls -l1 $PWD/plugins/nf-tower/build/libs/
nf-tower-0.1.0.jar
nf-tower-0.1.0.json
nf-tower-0.1.0.zip

Copies plugin dependencies jar files in the plugin build directory ie. $PWD/plugins/nf-amazon/build/target/libs. This is only needed when launching the plugin in development mode.

Copies the plugin zip file to the root project build dir ie. $PWD/build/plugins/.

Uploads the plugin ZIP and meta (JSON) files to the corresponding GitHub repository. Options:

• release: the plugin version e.g. 1.0.1
• repo: the GitHub repository name e.g. nf-amazon
• owner: the GitHub owning organization e.g. nextflow-io
• skipExisting: do not upload a file already existing (only if the checksum is the same, default: true).
• dryRun: execute the tasks without uploading file (default: false).
• overwrite: prevent to overwrite a remote file already existing (default: false).
• userName: the user name for authenticate GitHub API requests
• authToken: the personal token to authenticate GitHub API requests

Uploads the plugin both zip and meat files.

Upload the plugins index to the repository hosted at https://github.com/nextflow-io/plugins, which makes them accessible through the URL https://raw.githubusercontent.com/nextflow-io/plugins/main/plugins.json.

• https://pf4j.org/
• https://proandroiddev.com/understanding-gradle-the-build-lifecycle-5118c1da613f