nf-gadi Plugin

nf-gadi plugin provides a usage report for nextflow processes using NCI Gadi PBS Pro executor. To run this plugin, Nextflow version must >= 24.04.1.

Installation

Install from plugin registry

Start from v1.1.0, this plugin can be download from Nextflow plugin registry

module load nextflow/25.10.3
nextflow plugin install nf-gadi@1.2.0   

We recommend to download the plugin before running the workflow.

If you are using Nextflow < 25.10 and cannot download the latest version, add an additional plugin registry file before installation.

module load nextflow/24.04.1 

export NXF_PLUGINS_TEST_REPOSITORY="https://raw.githubusercontent.com/nextflow-io/plugins/ae0dc81429fbab18b1f98c6421c7ce5d92f71253/plugins.json"

nextflow plugin install nf-gadi@1.2.0 

Install from repository

To use this plugin in an offline environment, you will need to download and install this plugin on a system with an internet connection.

Clone the repository

git clone https://github.com/eileen-xue/nf-gadi.git

Build the plugin

cd nf-gadi
module load nextflow
make install

Settings

nf-gadi can provide json or csv output. Users can define the output format and output file name in the nextflow.config file. Both settings are optional. By default, the plugin generates a UsageReport.csv file. Do not change the output file name if requires to get cached usage report data with nextflow -resume.

gadi {
    format = 'csv'
    output = 'report.csv'
}

Run the plugin

There are two methods to run the Nextflow pipeline with the plugin

nextflow.config

Add the plugin to the configuration file

plugins {
    id 'nf-gadi@1.2.0'
}

Then run the Nextflow pipeline with nextflow run main.nf

Nextflow command

Another method to run the plugin is by adding it to the Nextflow command

nextflow run main.nf -plugins nf-gadi@1.2.0