{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "samtools_faidx",
  "description": "Indexes FASTA files to enable random access to fasta and fastq files.",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "description": "FASTA input file.\n",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
        },
        "length": {
          "type": "integer",
          "description": "Length for FASTA sequence line wrapping",
          "help_text": "Type: `integer`, multiple: `False`, default: `60`. ",
          "default": 60
        },
        "region_file": {
          "type": "string",
          "format": "path",
          "description": "File of regions",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Write output to file.\n",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.fasta\"`, direction: `output`, example: `\"output.fasta\"`. ",
          "default": "$id.$key.output.fasta"
        },
        "mark_strand": {
          "type": "string",
          "description": "Add strand indicator to sequence name",
          "help_text": "Type: `string`, multiple: `False`, default: `\"rc\"`. ",
          "default": "rc"
        },
        "fai_idx": {
          "type": "string",
          "format": "path",
          "description": "Read/Write to specified index file (default file.fa.fai).\n",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.fai_idx.fai\"`, direction: `output`, example: `\"file.fa.fai\"`. ",
          "default": "$id.$key.fai_idx.fai"
        },
        "gzi_idx": {
          "type": "string",
          "format": "path",
          "description": "Read/Write to specified compressed file index (used with .gz files, default file.fa.gz.gzi).\n",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.gzi_idx.gzi\"`, direction: `output`, example: `\"file.fa.gz.gzi\"`. ",
          "default": "$id.$key.gzi_idx.gzi"
        },
        "fastq": {
          "type": "boolean",
          "description": "Read FASTQ files and output extracted sequences in FASTQ format",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        }
      }
    },
    "options": {
      "title": "Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "continue": {
          "type": "boolean",
          "description": "Continue working if a non-existent region is requested.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "reverse_complement": {
          "type": "boolean",
          "description": "Reverse complement sequences.\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/options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
