Pipeline schema syntax

Pipelines should have a nextflow_schema.json file that describes the different pipeline parameters (eg. params.something, --something).


Reminder: you should generally never need to edit this JSON file by hand. The nf-core schema build command can create and edit the file for you to keep it up to date, with a friendly user-interface for customisation.

The lint test checks the schema for the following:

  • Schema should be a valid JSON file
  • Schema should adhere to JSONSchema, Draft 7.
  • Parameters can be described in two places:
    • As properties in the top-level schema object
    • As properties within subschemas listed in a top-level definitions objects
  • The schema must describe at least one parameter
  • There must be no duplicate parameter IDs across the schema and definition subschema
  • All subschema in definitions must be referenced in the top-level allOf key
  • The top-level allOf key must not describe any non-existent definitions
  • Default parameters in the schema must be valid
  • Core top-level schema attributes should exist and be set as follows:
    • $schema:
    • $id: URL to the raw schema file, eg.
    • title: YOURPIPELINE pipeline parameters
    • description: The pipeline config manifest.description
  • That the input property is defined and has a mimetype. A list of common mimetypes can be found here.

For example, an extremely minimal schema could look like this:

  "$schema": "",
  "$id": "",
  "title": "YOURPIPELINE pipeline parameters",
  "description": "This pipeline is for testing",
  "properties": {
    "first_param": { "type": "string" }
  "definitions": {
    "my_first_group": {
      "properties": {
        "second_param": { "type": "string" }
  "allOf": [{ "$ref": "#/definitions/my_first_group" }]

You can check your pipeline schema without having to run the entire pipeline lint by running nf-core schema lint instead of nf-core lint