nf-polly plugin

This project contains a Nextflow plugin called nf-polly which provides utilities for using the Polly platform developed by Elucidata.

Plugin structure

• settings.gradle – Gradle project settings.

• plugins/nf-polly – The plugin implementation base directory.

• plugins/nf-polly/build.gradle – Plugin Gradle build file. Project dependencies should be added here.

• plugins/nf-polly/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.polly.PollyPlugin.

• plugins/nf-polly/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-polly/src/main – The plugin implementation sources.

• plugins/nf-polly/src/test – The plugin unit tests.

Plugin classes

• PollyConfig – to handle options from the Nextflow configuration

• PollyExtension – contains custom utilities (operators, functions, etc.) for use in the Polly pipelines environment.

• PollyPlugin – the plugin entry point

Unit testing

To run your unit tests, run the following command in the project root directory (ie. where the file settings.gradle is located):

./gradlew check

Testing and debugging

To build and test the plugin during development, 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 assemble

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

   ./launch.sh run my_org/my_pipeline -plugins nf-polly

Publishing with a Nextflow installation

This plugin can be made available to a local Nextflow installation using the following steps:

1. Build the plugin: make buildPlugins
2. Copy build/plugins/nf-polly-1.2.3 to $HOME/.nextflow/plugins

To test, create a pipeline that uses the plugin and run it: nextflow run ./my-pipeline-script.nf