{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "bcftools_sort",
  "description": "Sort VCF/BCF file.\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input VCF/BCF file to sort.\n\nThe file to be sorted by genomic coordinates.\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.vcf.gz\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Write output to a file.\n\nIf not specified, output goes to standard output.\n",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.gz\"`, direction: `output`, example: `\"sorted.vcf.gz\"`. ",
          "default": "$id.$key.output.gz"
        }
      }
    },
    "options": {
      "title": "Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "output_type": {
          "type": "string",
          "description": "Output file type.\n\n**Options:**\n- u: uncompressed BCF\n- b: compressed BCF  \n- v: uncompressed VCF\n- z: compressed VCF\n- 0-9: compression level for compressed formats\n\n**Default:** v (uncompressed VCF)\n",
          "help_text": "Type: `string`, multiple: `False`, example: `\"z\"`. "
        },
        "verbosity": {
          "type": "integer",
          "description": "Verbosity level.\n\nHigher values increase verbosity of output messages.\n",
          "help_text": "Type: `integer`, multiple: `False`, example: `1`. "
        },
        "write_index": {
          "type": "string",
          "description": "Automatically index the output files.\n\n**Format:** Specify index format or use default.\n",
          "help_text": "Type: `string`, multiple: `False`, example: `\"tbi\"`. "
        }
      }
    },
    "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/inputs"
    },
    {
      "$ref": "#/$defs/outputs"
    },
    {
      "$ref": "#/$defs/options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
