{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "parallel_map",
  "description": "Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n",
  "type": "object",
  "$defs": {
    "input arguments": {
      "title": "Input arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input_r1": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "exists": true,
          "description": "Input FASTQ files for the forward reads",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`. "
        },
        "input_r2": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "exists": true,
          "description": "Input FASTQ files for the reverse reads",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`. "
        },
        "genomeDir": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Reference genome to match to",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "barcodesFasta": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "FASTA file where each entry specifies a unique barcode sequence present at the start of the forward input reads\n(input_r1)",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        }
      }
    },
    "barcode arguments": {
      "title": "Barcode arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "umiLength": {
          "type": "integer",
          "description": "Length of the Unique Molecular Identifiers (UMI)",
          "help_text": "Type: `integer`, multiple: `False`, required. "
        },
        "limitBAMsortRAM": {
          "type": "string",
          "description": "",
          "help_text": "Type: `string`, multiple: `False`, default: `\"10000000000\"`. ",
          "default": "10000000000"
        }
      }
    },
    "runtime arguments": {
      "title": "Runtime arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "runThreadN": {
          "type": "integer",
          "description": "Number of threads to use for a single STAR execution.",
          "help_text": "Type: `integer`, multiple: `False`, default: `1`. ",
          "default": 1
        }
      }
    },
    "output arguments": {
      "title": "Output arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "description": "A list of output folders which are the result of using STAR to map each input FASTQ pair STAR to the reference genome.\nThe order of the items DO NOT match with the order of the entries in the barcodes FASTA file or the input FASTQ pairs",
          "help_text": "Type: `file`, multiple: `True`, required, default: `[\"./*\"]`, direction: `output`. ",
          "default": [
            "./*"
          ]
        },
        "joblog": {
          "type": "string",
          "format": "path",
          "description": "Where to store the log file listing all the jobs.",
          "help_text": "Type: `file`, multiple: `False`, default: `\"execution_log.txt\"`, direction: `output`. ",
          "default": "execution_log.txt"
        }
      }
    },
    "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/barcode arguments"
    },
    {
      "$ref": "#/$defs/runtime arguments"
    },
    {
      "$ref": "#/$defs/output arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
