Summary

A Nextflow plugin to work with validation of pipeline parameters and sample sheets. This plugin provides functionality for:

• 📖 Print usage instructions to the terminal (for use with --help)
• ✍️ Print log output showing parameters with non-default values
• ✅ Validate supplied parameters against the pipeline schema
• 📋 Validate the contents of supplied sample sheet files
• 🛠️ Create a type-casted list from a parsed sample sheet

Supported sample sheet formats are CSV, TSV, JSON and YAML.

Get Started

Declare the plugin in your Nextflow pipeline configuration file:

plugins {
  id 'nf-schema@2.7.2'
}

This is all that is needed - Nextflow will automatically fetch the plugin code at run time. Always pin the plugin version to ensure your pipeline continues working when new versions with breaking changes are released.

Include the plugin helper functions into your Nextflow pipeline:

include { validateParameters; paramsSummaryLog; samplesheetToList } from 'plugin/nf-schema'

// Validate input parameters
validateParameters()

// Print summary of supplied parameters
log.info paramsSummaryLog(workflow)

// Create a new channel of metadata from a sample sheet passed to the pipeline through the --input parameter
ch_input = Channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))

Alternatively, enable the creation of the help message (using --help) in the configuration file:

validation {
  help {
    enabled = true
  }
}

Requirements:

• Java 17 or later
• Nextflow 25.10.0 or later

Examples

include { validateParameters; paramsSummaryLog; samplesheetToList } from 'plugin/nf-schema'

// Validate input parameters
validateParameters()

// Print summary of supplied parameters
log.info paramsSummaryLog(workflow)

// Create a new channel of metadata from a sample sheet passed to the pipeline through the --input parameter
ch_input = Channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))

License

Apache License 2.0. See the LICENSE file for details.