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'
}

You can now 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"))

Or 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