{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "fq_lint",
  "description": "Validates a single or paired FASTQ file.",
  "type": "object",
  "$defs": {
    "input": {
      "title": "Input",
      "type": "object",
      "description": "Input FASTQ files to validate.",
      "properties": {
        "input_1": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Read 1 source",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"reads_1.fastq.gz\"`. "
        },
        "input_2": {
          "type": "string",
          "format": "path",
          "description": "Read 2 source",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"reads_2.fastq.gz\"`. "
        }
      }
    },
    "options": {
      "title": "Options",
      "type": "object",
      "description": "Validation parameters.",
      "properties": {
        "lint_mode": {
          "type": "string",
          "description": "Panic on first error or log all errors.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"panic\"`, choices: ``panic`, `log``. ",
          "enum": [
            "panic",
            "log"
          ],
          "default": "panic"
        },
        "single_read_validation_level": {
          "type": "string",
          "description": "Only use single read validators up to a given level.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"high\"`, choices: ``low`, `medium`, `high``. ",
          "enum": [
            "low",
            "medium",
            "high"
          ],
          "default": "high"
        },
        "paired_read_validation_level": {
          "type": "string",
          "description": "Only use paired read validators up to a given level.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"high\"`, choices: ``low`, `medium`, `high``. ",
          "enum": [
            "low",
            "medium",
            "high"
          ],
          "default": "high"
        },
        "disable_validator": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "Disable validators by code",
          "help_text": "Type: `string`, multiple: `True`. "
        },
        "record_definition_separator": {
          "type": "string",
          "description": "Define a record definition separator.",
          "help_text": "Type: `string`, multiple: `False`. "
        }
      }
    },
    "nextflow input-output arguments": {
      "title": "Nextflow input-output arguments",
      "type": "object",
      "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
      "properties": {
        "publish_dir": {
          "type": "string",
          "description": "Path to an output directory.",
          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/$defs/input"
    },
    {
      "$ref": "#/$defs/options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
