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nf-openBIS Plugin

This project implements a nextflow plugin offering channel factories emitting and consuming openBIS objects.

NOTE: this repo is based on nf-hello. Documentation and certain files reflect this.

Plugin structure

  • settings.gradle

    Gradle project settings.

  • plugins/nf-hello

    The plugin implementation base directory.

  • plugins/nf-hello/build.gradle

    Plugin Gradle build file. Project dependencies should be added here.

  • plugins/nf-hello/src/resources/META-INF/MANIFEST.MF

    Manifest file defining the plugin attributes e.g. name, version, etc. The attribute Plugin-Class declares the plugin main class. This class should extend the base class nextflow.plugin.BasePlugin e.g. nextflow.openbis.OpenbisPlugin.

  • plugins/nf-hello/src/resources/META-INF/extensions.idx

    This file declares one or more extension classes provided by the plugin. Each line should contain the fully qualified name of a Java class that implements the org.pf4j.ExtensionPoint interface (or a sub-interface).

  • plugins/nf-hello/src/main

    The plugin implementation sources.

  • plugins/nf-hello/src/test

    The plugin unit tests.

Plugin classes

  • HelloConfig: simple example how to handle configuration options provided via the Nextflow configuration file.

  • HelloExtension: show how create an extension class that can be used to create custom channel factories, operation and fuctions that can be imported in the pipeline script as DSL extensions.

  • HelloFactory and HelloObserver: show how to intercept workflow runtime events and react correspondly with custom code.

  • HelloPlugin: the plugin entry point.

Unit testing

Run the following command in the project root directory (ie. where the file settings.gradle is located):

./gradlew check

Testing and debugging

To run and test the plugin in for development purpose, configure a local Nextflow build with the following steps:

  1. Clone the Nextflow repository in your computer into a sibling directory:

    git clone --depth 1 https://github.com/nextflow-io/nextflow ../nextflow

  2. Configure the plugin build to use the local Nextflow code:

    echo "includeBuild('../nextflow')" >> settings.gradle

    (Make sure to not add it more than once!)

  3. Compile the plugin alongside the Nextflow code:

    make compile

  4. Run Nextflow with the plugin, using ./launch.sh as a drop-in replacement for the nextflow command, and adding the option -plugins nf-hello to load the plugin:

    ./launch.sh run nextflow-io/hello -plugins nf-hello

Testing without Nextflow build

The plugin can be tested without using a local Nextflow build using those steps:

  1. generate required artifacts with make buildPlugins
  2. copy build/plugins/your-plugin to $HOME/.nextflow/plugins
  3. create a pipeline with your plugin and see in action via nextflow run ./my-pipeline-script.nf

Package, upload and publish

The project should be hosted in a GitHub repository whose name should match the name of the plugin, that is the name of the directory in the plugins folder (e.g. nf-hello).

Follow these steps to package, upload and publish the plugin:

  1. Create a file named gradle.properties in the project root containing the following attributes (this file should not be committed to Git):

    • github_organization: the GitHub organisation where the plugin repository is hosted.
    • github_username: The GitHub username granting access to the plugin repository.
    • github_access_token: The GitHub access token required to upload and commit changes to the plugin repository.
    • github_commit_email: The email address associated with your GitHub account.

  2. Use the following command to package and create a release for your plugin on GitHub:

    ./gradlew :plugins:nf-hello:upload

  3. Create a pull request against nextflow-io/plugins to make the plugin accessible to Nextflow.