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The plugin `nf-nextpie`

The project contains a Nextflow plugin (adapted from nf-plugin) called nf-nextpie which serves as a client for Nextpie server. The plugin uploads (trace.txt file) resource usage data from a nextflow pipeline to Nextpie for aggregated resource usage analysis and visualization.

The plugin readily comes with a config file plugins/nf-nextpie/src/main/nextflow/nextpie/config.json. It contains parameters needed for Nextpie with default values. The default config file assumes that Nextpie is running in localhost. The config file parameters can be modified according to one's need.

Config file

After the first use of the plugin in Nextflow using -plugins nf-nextpie@0.0.1, Nextflow will download the plugin to $HOME/.nextflow/plugins/nf-nextpie-0.0.1. The config file will be found from $HOME/.nextflow/plugins/nf-nextpie-0.0.1/classes/nextflow/nextpie/config.json. Following is the content of config.json.

{
  "host": "localhost",
  "port": 5000,
  "api-key": "jWCr-uqJB9fO9s1Lj2QiydXs4fFY2M",
  "workflow-name-var" : "workflow_name",
  "worfklow-version-var" : "workflow_ver"
}

`host`

This is a hostname/IP address of a machine running Nextpie. The default value is localhost which meaning you should be running Nextpie in the current machine.

`port`

This is the port in which Nextpie is running. Do not change the port until and unless you know what you are doing.

`api-key`

This is a API key need for authntication. Using this key the client (nf-plugin) authenticates itself with Nextpie server. In production use, generate an unique API key from Nextpie's GUI and replace the defaut one. This is highly recommend for security reasons.

`workflow-name-var` and `worfklow-version-var`

This is the name of Nextflow variable you used in the pipeline to store pipeline name. The default calue is workflow_name which means you have a variable named workflow_name in your Nextflow pipeline (eg. in nextflow.config). You can change the value workflow_name in $HOME/.nextflow/plugins/nf-nextpie-0.0.1/classes/nextflow/nextpie/config.json if you have different variable. Similary, the worfklow-version-var contains a variable name (default: workflow_ver) used in Nextflow pipeline to store pipeline version. This can also be changed according to your need.

Then default config parameters can be overwritten by provided commandline parameters --host, --port, --api_key, --workflow_name, and --workflow_ver via Nextflow's commandline. The following is an example.

/PATH/TO/nextflow run /path/to/main.nf \
  --host 192.168.0.5 \
  --port 80 \
  --api_key HGnm4sdfiJHH06 \
  --workflow_name myPipeline \
  --workflow_ver 0.0.1
  ....

Plugin structure

├── plugins
│   ├── build.gradle
│   └── nf-nextpie                          #The plugin base directory.
│       ├── build.gradle                    #Plugin Gradle build file.
│       └── src
│          ├── main                        #The plugin implementation sources.
│          │   └── nextflow
│          │       └── nextpie
│          │           ├── config.json
│          │           ├── nextpieFactory.groovy
│          │           ├── nextpieObserver.groovy
│          │           └── nextpiePlugin.groovy
│          ├── 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.
│          │       │
│          │       └── 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.nextpie.nextpiePlugin`.
│          │
│          └── test                         #The plugin unit tests.                  
│              └── nextflow
│                  └── nextpie
│                      ├── HelloDslTest.groovy
│                      ├── MockHelpers.groovy
│                      ├── nextpieFactoryTest.groovy
│                      └── TestHelper.groovy
│       
├── README.md
└──  settings.gradle                         #Gradle project settings.

Plugin classes

nextpieFactory and nextpieObserver: shows how to react to workflow events with custom behavior
nextpiePlugin: the plugin entry point

Running the plugin

Clone the Nextpie repository:

cd $HOME
git clone https://github.com/bishwaG/Nextpie.git

Configure the plugin build to use the local Nextflow code:
```
cd Nextpie/assets/example-workflow/test-runs/
```
Run the Nextflow example workflow that comes with Nextpie.

./nextflow run \
   ../main.nf \
   --fastqs 'fastq/*_R{1,2}*.fastq.gz' \
   --name "test_project" \
   --group "test_research_group" \
   -resume

NOTE: $HOME/Nextpie/cd assets/example-workflow/nextflow.config contains plugins { id 'nf-nextpie' } which will tell Nextflow to pull nf-nextpie during a runtime. The config file nextflow.config also contains variables workflow_name to store pipeline name and workflow_ver to store pipeline version.

Integrating `nf-nextpie` with a Nextflow pipeline.

To use the plugin in any Nexflow pipleine add the following content in nextflow.config file of your Nextflow pipeline. This way the pipeline will use the plugin during every run.

plugins {
  id 'nf-nextpie'
}

If you do not want to ad the plugin to a pipeline, but want to use in run-by-run basis provide -plugins nf-nextpie@0.0.1 parameter in Nextflow's command-line.

Building and installing the plugin

## Clone the repo
git clone https://github.com/bishwaG/nf-nextpie.git

## Unit testing
make check

## build the plugin
make

## Install the plugin
## Installs to $HOME/.nextflow/plugins
make install

## Upload to Git and make a version release
make upload

Releases

Release	Date	Downloads	Author
0.0.1	2025-03-16	17	bishwaG

Downloads

The plugin nf-nextpie