{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "umi_tools_prepareforrsem",
  "description": "Make the output from umi-tools dedup or group compatible with RSEM",
  "type": "object",
  "$defs": {
    "input": {
      "title": "Input",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"$id.transcriptome.bam\"`. "
        }
      }
    },
    "output": {
      "title": "Output",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.bam\"`, direction: `output`, example: `\"$id.transcriptome_sorted.bam\"`. ",
          "default": "$id.$key.output.bam"
        },
        "log": {
          "type": "string",
          "format": "path",
          "description": "File with logging information [default = stdout].",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.log\"`, direction: `output`. ",
          "default": "$id.$key.log"
        },
        "error": {
          "type": "string",
          "format": "path",
          "description": "File with error information [default = stderr].",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.error\"`, direction: `output`. ",
          "default": "$id.$key.error"
        },
        "log2stderr": {
          "type": "boolean",
          "description": "Send logging information to stderr [default = False].",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "temp_dir": {
          "type": "string",
          "description": "Directory for temporary files",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "compresslevel": {
          "type": "integer",
          "description": "Level of Gzip compression to use",
          "help_text": "Type: `integer`, multiple: `False`. "
        }
      }
    },
    "options": {
      "title": "Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "tags": {
          "type": "string",
          "description": "Comma-seperated list of tags to transfer from read1 to read2 (Default: 'UG,BX')\n",
          "help_text": "Type: `string`, multiple: `False`, example: `\"UG,BX\"`. "
        },
        "sam": {
          "type": "boolean",
          "description": "Input and output SAM rather than BAM.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "timeit": {
          "type": "string",
          "description": "Store timeing information in file [none].\n",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "timeit_name": {
          "type": "string",
          "description": "Name in timing file for this class of jobs [all].\n",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "timeit_header": {
          "type": "boolean",
          "description": "Add header for timing information [none].",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "verbose": {
          "type": "integer",
          "description": "Loglevel [1]",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "random_seed": {
          "type": "integer",
          "description": "Random seed to initialize number generator with [none].\n",
          "help_text": "Type: `integer`, multiple: `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"
    },
    {
      "$ref": "#/$defs/output"
    },
    {
      "$ref": "#/$defs/options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
