π Docs ππ» https://nextflow-io.github.io/nf-validation
A Nextflow plugin to work with validation of pipeline parameters and sample sheets.
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:
- π Print usage instructions to the terminal (for use with
--help
) - βοΈ Print log output showing parameters with non-default values
- β Validate supplied parameters against the pipeline schema
- π Validate the contents of supplied sample sheet files
- π οΈ Create a Nextflow channel with a parsed sample sheet
Supported sample sheet formats are CSV, TSV, JSON and YAML.
Declare the plugin in your Nextflow pipeline configuration file:
plugins {
id 'nf-validation'
}
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 latest version, good to make sure
that the latest bug fixes are included! However, this can cause difficulties if running
offline. You can pin a specific release using the syntax [email protected]
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")
- Java 11 or later
- https://github.com/harrel56/json-schema
There is a dedicated nf-validation Slack channel in the Nextflow Slack workspace.
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):
- JΓΊlia Mir Pedrol (@mirpedrol)
- Nicolas Vannieuwkerke (@nvnieuwk)
- Kevin Menden (@KevinMenden)
- Phil Ewels (@ewels)
- Arthur (@awgymer)