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📚 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:
```groovy title="nextflow.config" plugins { id 'nf-schema@2.4.1' }
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:
```groovy title="main.nf"
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:
groovy title="nextflow.config"
validation {
help {
enabled: true
}
}
Dependencies
- Java 11 or later
- https://github.com/harrel56/json-schema
- Nextflow 24.10.0 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)
Releases
| Release | Date | Downloads | Author |
|---|---|---|---|
| 2.4.2 | 2025-05-07 | 2729 | nvnieuwk |
| 2.4.1 | 2025-04-10 | 1459 | nvnieuwk |
| 2.4.0 | 2025-04-03 | 417 | nvnieuwk |
| Hakodate | 2025-01-13 | 77906 | nvnieuwk |
| 2.2.1 | 2024-12-03 | 13463 | nvnieuwk |
| Kitakata | 2024-10-30 | 28939 | nvnieuwk |
| 2.1.2 | 2024-10-18 | 8555 | nvnieuwk |
| 2.1.1 | 2024-09-19 | 95140 | nvnieuwk |
| Tantanmen | 2024-08-20 | 10842 | nvnieuwk |
| 2.0.1 | 2024-07-04 | 1432 | nvnieuwk |
| Kagoshima | 2024-04-22 | 16888 | nvnieuwk |