schema_lint

PipelineLint.schema_lint()

Pipeline schema syntax

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

The lint test checks the schema for the following:

• Schema should be a valid JSON file

• Schema should adhere to JSONSchema, Draft 7 or Draft 2020-12.

• 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``(draft 7) or

  ``

  $defs``(draft 2020-12) 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 or $defs 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: https://json-schema.org/draft-07/schema or https://json-schema.org/draft/2020-12/schema
  • $id: URL to the raw schema file, eg. https://raw.githubusercontent.com/YOURPIPELINE/master/nextflow_schema.json
  • 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 (draft 7):

{
  "$schema": "https://json-schema.org/draft-07/schema",
  "$id": "https://raw.githubusercontent.com/YOURPIPELINE/master/nextflow_schema.json",
  "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" }]
}

Or this (draft 2020-12):

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://raw.githubusercontent.com/YOURPIPELINE/master/nextflow_schema.json",
  "title": "YOURPIPELINE pipeline parameters",
  "description": "This pipeline is for testing",
  "properties": {
    "first_param": { "type": "string" }
  },
  "$defs": {
    "my_first_group": {
      "properties": {
        "second_param": { "type": "string" }
      }
    }
  },
  "allOf": [{ "$ref": "#/$defs/my_first_group" }]
}