{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "build_star_reference",
  "description": "Create a reference for STAR from a set of fasta files.",
  "type": "object",
  "$defs": {
    "input/output": {
      "title": "Input/Output",
      "type": "object",
      "description": "No description",
      "properties": {
        "genome_fasta": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "exists": true,
          "description": "The fasta files to be included in the reference",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"chr1.fasta\";\"chr2.fasta\"]`. "
        },
        "transcriptome_gtf": {
          "type": "string",
          "format": "path",
          "description": "Specifies the path to the file with annotated transcripts in the standard GTF\nformat",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"transcriptome.gtf\"`. "
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "Path to output directory",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`, example: `\"/path/to/foo\"`. ",
          "default": "$id.$key.output"
        }
      }
    },
    "genome indexing arguments": {
      "title": "Genome indexing arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "genomeSAindexNbases": {
          "type": "integer",
          "description": "Length (bases) of the SA pre-indexing string",
          "help_text": "Type: `integer`, multiple: `False`, default: `14`. ",
          "default": 14
        }
      }
    },
    "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/output"
    },
    {
      "$ref": "#/$defs/genome indexing arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
