{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "cellranger_mkgtf",
  "description": "Make a GTF file - filter by a specific attribute.",
  "type": "object",
  "$defs": {
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input_gtf": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Reference GTF annotation.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"transcriptome_annotation.gtf.gz\"`. "
        },
        "output_gtf": {
          "type": "string",
          "format": "path",
          "description": "Output GTF file.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output_gtf.gz\"`, direction: `output`, example: `\"output.gtf.gz\"`. ",
          "default": "$id.$key.output_gtf.gz"
        },
        "attribute": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "Key-value pair in attributes field to be kept in the GTF file of the format attribute:attribute_value.",
          "help_text": "Type: `string`, multiple: `True`, required, example: `[\"gene_type:transcribed_unprocessed_pseudogene\";\"gene_type:miRNA\"]`. "
        }
      }
    },
    "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/arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
