mirpedrol/nf-validation

Params validation plugin for Nextflow pipelines

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

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

Introduction

This Nextflow plugin provides a number of functions that can be included into a Nextflow pipeline script to work with parameter and sample sheet schema. Using these functions you can:

• 📖 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 Nextflow channel with a parsed sample sheet

Supported sample sheet formats are CSV, TSV and YAML (simple).

Quick Start

Declare the plugin in your Nextflow pipeline configuration file:

(make sure you pin the latest stable release version after the @)

plugins {
  id '[email protected]'
}

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

You can now include the plugin helper functions into your Nextflow pipeline:

include { validateParameters; paramsHelp; paramsSummaryLog; fromSamplesheet } from 'plugin/nf-validation'

// Print help message, supply typical command line usage for the pipeline
if (params.help) {
   log.info paramsHelp("nextflow run my_pipeline --input input_file.csv")
   exit 0
}

// Validate input parameters
validateParameters()

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

// Create a new channel of metadata from a sample sheet
// NB: `input` corresponds to `params.input` and associated sample sheet schema
ch_input = Channel.fromSamplesheet("input")

Dependencies

• Java 11 or later
• https://github.com/everit-org/json-schema

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)