📚 Docs 👉🏻 https://nextflow-io.github.io/nf-schema

A Nextflow plugin to work with validation of pipeline parameters and sample sheets.

Introduction

Important

nf-schema is the new version of the now deprecated nf-validation. Please follow the migration guide to migrate your code to this new version.

This Nextflow plugin provides functionality that can be used in a Nextflow pipeline to work with parameter and sample sheet schema. The added functionality is:

• 📖 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.

Quick Start

Declare the plugin in your Nextflow pipeline configuration file:

plugins {
  id 'nf-schema@2.2.0'
}

This is all that is needed - Nextflow will automatically fetch the plugin code at run time.

Note

The snippet above will always try to install the specified version. We encourage always pinning the plugin version to make sure the used pipeline will keep working when a new version of nf-schema with breaking changes has been released.

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
  }
}

Dependencies

• Java 11 or later
• https://github.com/harrel56/json-schema
• Nextflow 23.10.0 or later

Slack channel

There is a dedicated nf-schema Slack channel in the Nextflow Slack workspace.

Credits

This plugin was written based on code initially written within the nf-core community, as part of the nf-core pipeline template.

We would like to thank the key contributors who include (but are not limited to):

• Júlia Mir Pedrol (@mirpedrol)
• Nicolas Vannieuwkerke (@nvnieuwk)
• Kevin Menden (@KevinMenden)
• Phil Ewels (@ewels)
• Arthur (@awgymer)