{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "runner",
  "description": "Runner for demultiplexing of raw sequencing data",
  "type": "object",
  "$defs": {
    "input arguments": {
      "title": "Input arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Base directory of the canonical form `s3://<bucket>/<path>/<RunID>/`.\nA tarball (tar.gz, .tgz, .tar) containing run information can be provided.\nThe <RunID> is the value passed to the `id` argument.\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "run_information": {
          "type": "string",
          "format": "path",
          "description": "CSV file containing sample information, which will be used as \ninput for the demultiplexer",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
        },
        "demultiplexer": {
          "type": "string",
          "description": "Demultiplexer to use, choice depends on the provider\nof the instrument that was used to generate the data.\nWhen not using --sample_sheet, specifying this argument is not\nrequired.\n",
          "help_text": "Type: `string`, multiple: `False`, choices: ``bases2fastq`, `bclconvert``. ",
          "enum": [
            "bases2fastq",
            "bclconvert"
          ]
        }
      }
    },
    "annotation flags": {
      "title": "Annotation flags",
      "type": "object",
      "description": "No description",
      "properties": {
        "plain_output": {
          "type": "boolean",
          "description": "Flag to indicate that the output should be stored directly under $publish_dir rather than\nunder a subdirectory structure runID/<date_time>_demultiplex_<version>/.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        }
      }
    },
    "output arguments": {
      "title": "Output arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "fastq_output": {
          "type": "string",
          "format": "path",
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, default: `\"fastq\"`, direction: `output`. ",
          "default": "fastq"
        },
        "sample_qc_output": {
          "type": "string",
          "format": "path",
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, default: `\"qc/fastqc\"`, direction: `output`. ",
          "default": "qc/fastqc"
        },
        "multiqc_output": {
          "type": "string",
          "format": "path",
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, default: `\"qc/multiqc_report.html\"`, direction: `output`. ",
          "default": "qc/multiqc_report.html"
        },
        "demultiplexer_logs": {
          "type": "string",
          "format": "path",
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, default: `\"demultiplexer_logs\"`, direction: `output`. ",
          "default": "demultiplexer_logs"
        }
      }
    },
    "other arguments": {
      "title": "Other arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "skip_copycomplete_check": {
          "type": "boolean",
          "description": "Disable the check for the presence of a \"CopyComplete.txt\" file in input\ndirectory in case of Illumina data.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": 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": "#/$defs/input arguments"
    },
    {
      "$ref": "#/$defs/annotation flags"
    },
    {
      "$ref": "#/$defs/output arguments"
    },
    {
      "$ref": "#/$defs/other arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}