{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "bowtie2_inspect",
  "description": "Extract information from Bowtie2 index files.\n\nBy default, prints FASTA records of the indexed nucleotide sequences to\nstandard output. With -n, just prints names. With -s, just prints a summary of\nthe index parameters and sequences.\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "index": {
          "type": "string",
          "description": "bt2 filename minus trailing .1.bt2/.2.bt2",
          "help_text": "Type: `string`, multiple: `False`, required, example: `\"genome_index\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Save output to filename (default stdout)",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.fasta\"`, direction: `output`, example: `\"sequences.fasta\"`. ",
          "default": "$id.$key.output.fasta"
        }
      }
    },
    "output options": {
      "title": "Output Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "summary": {
          "type": "boolean",
          "description": "Print summary incl",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "names": {
          "type": "boolean",
          "description": "Print reference sequence names only",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "across": {
          "type": "integer",
          "description": "Number of characters across in FASTA output (default 60)",
          "help_text": "Type: `integer`, multiple: `False`, example: `80`. "
        },
        "verbose_inspect": {
          "type": "boolean",
          "description": "Verbose output (for debugging)",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "debug": {
          "type": "boolean",
          "description": "Use the debug binary; slower, assertions enabled",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "sanitized": {
          "type": "boolean",
          "description": "Use sanitized binary; slower, uses ASan and/or UBSan",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "verbose": {
          "type": "boolean",
          "description": "Log the issued command",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        }
      }
    },
    "index options": {
      "title": "Index Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "large_index": {
          "type": "boolean",
          "description": "Force inspection of the 'large' index, even if a 'small' one is present",
          "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/output options"
    },
    {
      "$ref": "#/$defs/index options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
