{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "vireo",
  "description": "Vireo is primarily designed for demultiplexing cells into donors by modelling of expressed alleles.",
  "type": "object",
  "$defs": {
    "input": {
      "title": "Input",
      "type": "object",
      "description": "No description",
      "properties": {
        "cell_data": {
          "type": "string",
          "format": "path",
          "description": "The cell genotype file in VCF format or cellSNP folder with sparse matrices.",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
        },
        "n_donor": {
          "type": "integer",
          "description": "Number of donors to demultiplex; can be larger than provided in donor_file.",
          "help_text": "Type: `integer`, multiple: `False`, default: `2`. ",
          "default": 2
        },
        "vartrix_data": {
          "type": "string",
          "format": "path",
          "description": "The cell genotype files in vartrix outputs.",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
        },
        "donor_file": {
          "type": "string",
          "format": "path",
          "description": "The donor genotype file in VCF format",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
        },
        "geno_tag": {
          "type": "string",
          "description": "The tag for donor genotype.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"PL\"`, choices: ``GT`, `GP`, `PL``. ",
          "enum": [
            "GT",
            "GP",
            "PL"
          ],
          "default": "PL"
        },
        "no_doublet": {
          "type": "boolean",
          "description": "If use, not checking doublets.",
          "help_text": "Type: `boolean`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "n_init": {
          "type": "integer",
          "description": "Number of random initializations, when GT needs to learn.",
          "help_text": "Type: `integer`, multiple: `False`, default: `50`. ",
          "default": 50
        },
        "extra_donor": {
          "type": "integer",
          "description": "Number of extra donor in pre-cluster, when GT needs to learn.",
          "help_text": "Type: `integer`, multiple: `False`, default: `0`. ",
          "default": 0
        },
        "extra_donorMode": {
          "type": "string",
          "description": "Method for searching from extra donors",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "force_learn_gt": {
          "type": "boolean",
          "description": "If use, treat donor GT as prior only.",
          "help_text": "Type: `boolean`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "ase_mode": {
          "type": "boolean",
          "description": "If use, turn on SNP specific allelic ratio.",
          "help_text": "Type: `boolean`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "no_plot": {
          "type": "boolean",
          "description": "If use, turn off plotting GT distance.",
          "help_text": "Type: `boolean`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "rand_seed": {
          "type": "integer",
          "description": "Seed for random initialization",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "cell_range": {
          "type": "string",
          "description": "Range of cells to process.",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "call_ambient_rnas": {
          "type": "boolean",
          "description": "If use, detect ambient RNAs in each cell.",
          "help_text": "Type: `boolean`, multiple: `False`, default: `false`. ",
          "default": false
        }
      }
    },
    "output": {
      "title": "Output",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output directory",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output\"`, direction: `output`, example: `\"vireo\"`. ",
          "default": "$id.$key.output"
        }
      }
    },
    "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/nextflow input-output arguments"
    }
  ]
}
