{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "bcftools",
  "description": "Filter the variants called by freebayes or cellSNP",
  "type": "object",
  "$defs": {
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "vcf": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "exists": true,
          "description": "VCF files, must have the same sample columns appearing in the same order.",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`. "
        },
        "concat": {
          "type": "boolean",
          "description": "Concatenate or combine VCFs and sort them.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "filter": {
          "type": "boolean",
          "description": "Filter VCFs.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "filter_qual": {
          "type": "integer",
          "description": "Filter VCFs with specified QUAL threshold.",
          "help_text": "Type: `integer`, multiple: `False`, default: `30`. ",
          "default": 30
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "bcftools output directory",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output\"`, direction: `output`, example: `\"bcftools_out\"`. ",
          "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/arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
