{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "htrnaseq",
  "description": "No description",
  "type": "object",
  "$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`. "
        },
        "umi_length": {
          "type": "integer",
          "description": "Length of the UMI sequences\n",
          "help_text": "Type: `integer`, multiple: `False`, default: `10`. ",
          "default": 10
        },
        "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`. "
        },
        "sample_id": {
          "type": "string",
          "description": "Sample ID for the provided input files",
          "help_text": "Type: `string`, multiple: `False`. "
        }
      }
    },
    "output arguments": {
      "title": "Output arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "fastq_output": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "description": "Directory containing output fastq files",
          "help_text": "Type: `file`, multiple: `True`, required, default: `[\"fastq/*\"]`, direction: `output`. ",
          "default": [
            "fastq/*"
          ]
        },
        "star_output": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "description": "Output from mapping with STAR",
          "help_text": "Type: `file`, multiple: `True`, required, default: `[\"star.$id/*\"]`, direction: `output`. ",
          "default": [
            "star.$id/*"
          ]
        },
        "nrReadsNrGenesPerChrom": {
          "type": "string",
          "format": "path",
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"nrReadsNrGenesPerChrom.$id.txt\"`, direction: `output`. ",
          "default": "nrReadsNrGenesPerChrom.$id.txt"
        },
        "star_qc_metrics": {
          "type": "string",
          "format": "path",
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"starLogs.$id.txt\"`, direction: `output`. ",
          "default": "starLogs.$id.txt"
        },
        "eset": {
          "type": "string",
          "format": "path",
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"eset.$id.rds\"`, direction: `output`. ",
          "default": "eset.$id.rds"
        },
        "f_data": {
          "type": "string",
          "format": "path",
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"fData.$id.tsv\"`, direction: `output`. ",
          "default": "fData.$id.tsv"
        },
        "p_data": {
          "type": "string",
          "format": "path",
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"pData.$id.tsv\"`, direction: `output`. ",
          "default": "pData.$id.tsv"
        },
        "html_report": {
          "type": "string",
          "format": "path",
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"report.$id.html\"`, direction: `output`. ",
          "default": "report.$id.html"
        },
        "run_params": {
          "type": "string",
          "format": "path",
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, default: `\"params.$id.yaml\"`, direction: `output`. ",
          "default": "params.$id.yaml"
        }
      }
    },
    "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"
    }
  ]
}
