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/25.10.4
nextflow plugin install nf-gadi@1.3.1   

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/7e1c884584176121c5da63b5d37b0af2cc58f9b2/plugins.json"

nextflow plugin install nf-gadi@1.3.1 

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'
}

Alternatively, to generate separate reports each time the pipeline is run, you can add a timestamp parameter and use that in your output file name.

params {
	timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
}

gadi {
    format = 'csv'
    output = "report_${params.timestamp}.csv"
}

Optional: Publishing the report to an external location

By default, the usage report is written only to the path set in output.

Optionally, set publishTo to have the finished report copied to an external location once the workflow completes — anything Nextflow can resolve as a Path, such as s3://, gs://, or az://, given the relevant credentials/plugin are configured.

gadi {
    format    = 'csv'
    output    = "report.csv"
    publishTo = "s3://bucket/results/UsageReport.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@1.3.1'
}

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@1.3.1