{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "runner",
  "description": "Runner for HT RNA-seq pipeline",
  "type": "object",
  "$defs": {
    "input arguments": {
      "title": "Input arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Base directory of the form `s3:/<bucket>/Sequencing/<Sequencer>/<RunID>/<demultiplex_dir>`",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "barcodesFasta": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "genomeDir": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "annotation": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "ignore": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "Pool names to ignore.",
          "help_text": "Type: `string`, multiple: `True`, default: `[\"Undetermined\"]`. ",
          "default": [
            "Undetermined"
          ]
        },
        "umi_length": {
          "type": "integer",
          "description": "Length of the UMI sequences\n",
          "help_text": "Type: `integer`, multiple: `False`, default: `10`. ",
          "default": 10
        },
        "run_params": {
          "type": "string",
          "format": "path",
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, default: `\"params.yaml\"`, direction: `output`. ",
          "default": "params.yaml"
        }
      }
    },
    "metadata arguments": {
      "title": "Metadata arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "id": {
          "type": "string",
          "description": "Unique identifier for the run",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "project_id": {
          "type": "string",
          "description": "Project ID",
          "help_text": "Type: `string`, multiple: `False`, required. "
        },
        "experiment_id": {
          "type": "string",
          "description": "Experiment ID",
          "help_text": "Type: `string`, multiple: `False`, required. "
        }
      }
    },
    "publish arguments": {
      "title": "Publish arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "fastq_publish_dir": {
          "type": "string",
          "description": "",
          "help_text": "Type: `string`, multiple: `False`, required. "
        },
        "results_publish_dir": {
          "type": "string",
          "description": "",
          "help_text": "Type: `string`, multiple: `False`, required. "
        }
      }
    },
    "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/metadata arguments"
    },
    {
      "$ref": "#/$defs/publish arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
