{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "lofreq_indelqual",
  "description": "Insert indel qualities into BAM file (required for indel predictions).\n\nThe preferred way of inserting indel qualities should be via GATK's BQSR (>=2) If that's not possible, use this subcommand.\nThe command has two modes: 'uniform' and 'dindel':\n- 'uniform' will assign a given value uniformly, whereas\n- 'dindel' will insert indel qualities based on Dindel (PMID 20980555).\nBoth will overwrite any existing values.\nDo not realign your BAM file afterwards!\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input BAM file.\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"normal.bam\"`. "
        },
        "ref": {
          "type": "string",
          "format": "path",
          "description": "Reference sequence used for mapping (Only required for --dindel).\n",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"reference.fasta\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "out": {
          "type": "string",
          "format": "path",
          "description": "Output BAM file.\n",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.out.bam\"`, direction: `output`, example: `\"output.bam\"`. ",
          "default": "$id.$key.out.bam"
        }
      }
    },
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "uniform": {
          "type": "string",
          "description": "Add this indel quality uniformly to all bases",
          "help_text": "Type: `string`, multiple: `False`, example: `\"50,50\"`. "
        },
        "dindel": {
          "type": "boolean",
          "description": "Add Dindel's indel qualities (Illumina specific) (clashes with -u; needs --ref).\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "verbose": {
          "type": "boolean",
          "description": "Be verbose.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": 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/inputs"
    },
    {
      "$ref": "#/$defs/outputs"
    },
    {
      "$ref": "#/$defs/arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
