{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "kallisto_index",
  "description": "Build a Kallisto index for the transcriptome to use Kallisto in the mapping-based mode.\n",
  "type": "object",
  "$defs": {
    "input": {
      "title": "Input",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Path to a FASTA-file containing the transcriptome sequences, either in plain text or \ncompressed (.gz) format.\n",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
        },
        "d_list": {
          "type": "string",
          "format": "path",
          "description": "Path to a FASTA-file containing sequences to mask from quantification.\n",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
        }
      }
    },
    "output": {
      "title": "Output",
      "type": "object",
      "description": "No description",
      "properties": {
        "index": {
          "type": "string",
          "format": "path",
          "description": "",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.index\"`, direction: `output`, example: `\"Kallisto_index\"`. ",
          "default": "$id.$key.index"
        }
      }
    },
    "options": {
      "title": "Options",
      "type": "object",
      "description": "No description",
      "properties": {
        "kmer_size": {
          "type": "integer",
          "description": "Kmer length passed to indexing step of pseudoaligners (default: '31').\n",
          "help_text": "Type: `integer`, multiple: `False`, example: `31`. "
        },
        "make_unique": {
          "type": "boolean",
          "description": "Replace repeated target names with unique names.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "aa": {
          "type": "boolean",
          "description": "Generate index from a FASTA-file containing amino acid sequences.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "distiguish": {
          "type": "boolean",
          "description": "Generate index where sequences are distinguished by the sequence names.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "min_size": {
          "type": "integer",
          "description": "Length of minimizers (default: automatically chosen).\n",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "ec_max_size": {
          "type": "integer",
          "description": "Maximum number of targets in an equivalence class (default: no maximum).\n",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "tmp": {
          "type": "string",
          "description": "Path to a directory for temporary files.\n",
          "help_text": "Type: `string`, multiple: `False`, example: `\"tmp\"`. "
        }
      }
    },
    "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/input"
    },
    {
      "$ref": "#/$defs/output"
    },
    {
      "$ref": "#/$defs/options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
