nf-plugin-template is a gradle template to create Nextflow plugins

You can grab the template from:

https://github.com/jagedn/nf-plugin-template/

Features

  • minimal changes

  • simple structure, oriented to a single plugin

  • gradle 8.4

  • custom Gradle tasks included

  • ready to publish GitHub releases

  • asciidoctor documentation + GitHub Pages

Changes

This is a fork of the original jagedn/nf-plugin-template repository. In case you’re using original repo this new repo contains:

  • use gradle.properties to configure required variables

  • publish releases using JReleaser

Steps

  • Create a new Github project using this template

  • Clone in a directory with the name of your new plugin, i.e. nf-my-awesome-plugin

  • configure all details about your project:

gradle.properties
publish_description = An unofficial template to build Nextflow Plugins
publish_url = https://github.com/edn-es/nf-plugin-template
publish_year = 2023
publish_developer = jagedn
publish_developerName = Jorge Aguilera
publish_git = scm:git:https://github.com/edn-es/nf-plugin-template.git
publish_repoOwner = edn-es

  • add your dependencies. For example, add apache poi libs from mavenCentral

nf-plugin.gradle
dependencies {
    // add your dependencies, for example:
    implementation 'org.apache.poi:poi:5.2.4'
    implementation 'org.apache.poi:poi-ooxml:5.2.4'
}

  • rename src/main/groovy/com/nextflow/plugin directory and ExamplePlugin.groovy file with the package and name of your plugin

  • rename ExamplePlugin with a better name (for example MyAwesomePlugin)

  • delete/rename/update the ExampleFunctions.groovy with your extension

You don’t need to create the extensions points file (src/main/resources/META-INF/extensions.idx) as registerIdx task will scan your sources and build it

and this is all, you can run for example ./gradlew jsonPlugin to generate Nextflow’s artifacts

Configuration

This template includes an ExampleConfiguration to show you how to make your plugin configurable

Test

You can/need to create as many tests you consider. This template includes a full example running a pipeline and checking the result

Tasks

INFO

You can find new gradle tasks in nextflow group

  • generateIdx, scan sources and generate the extensions.idx resource

  • zipPlugin , compile and package your plugin in a zip file ready to be used by Nextflow

  • unzipPlugin , extract the zip file into your $HOME/.nextflow/plugins so you can use it in pipelines

  • jsonPlugin, create the json spec required by nextflow to publish a plugin

A typical scenario can be, once you’ve created/implemented some logic in your plugin, you’ve created some test but want to see in action in a pipeline. You can run the unzipPlugin task, and it will install the plugin into your $HOME/.nextflow/plugin directory

Or you can run the pipeline using the NXF_PLUGINS_TEST_REPOSITORY env with your build/plugins directory

Documentation

This template include asciidoctor gradle plugin to generate documentation.

You can write your documentation at src/docs/asciidoc and run ./gradlew asciidoctor to build it at build/doc directory.

Remember to prepare your GitHub repository with GH Pages (go to Settings, Pages and select GitHub Actions as source) and your documentation will be published automagically

Release

This template uses JReleaser to publish releases in GitHub (publish in MavenCentral soon). Also you can use the release GitHub action to run it (it only requires you specify which version are you deploying)