{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "well_demultiplex",
  "description": "Demultiplexing on well level",
  "type": "object",
  "$defs": {
    "input arguments": {
      "title": "Input arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input_r1": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "exists": true,
          "description": "Forward reads in FASTQ format",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`. "
        },
        "input_r2": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "exists": true,
          "description": "Reverse reads in FASTQ format",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`. "
        },
        "barcodesFasta": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        }
      }
    },
    "output arguments": {
      "title": "Output arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "output_r1": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "description": "List of demultiplexed fastq files",
          "help_text": "Type: `file`, multiple: `True`, required, default: `[\"fastq/*_R1_001.fastq\"]`, direction: `output`. ",
          "default": [
            "fastq/*_R1_001.fastq"
          ]
        },
        "output_r2": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "description": "List of demultiplexed fastq files",
          "help_text": "Type: `file`, multiple: `True`, required, default: `[\"fastq/*_R2_001.fastq\"]`, direction: `output`. ",
          "default": [
            "fastq/*_R2_001.fastq"
          ]
        }
      }
    },
    "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 arguments"
    },
    {
      "$ref": "#/$defs/output arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
