{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "combine_star_logs",
  "description": "No description",
  "type": "object",
  "$defs": {
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "barcodes": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "Barcodes responding to the respective log files.\n",
          "help_text": "Type: `string`, multiple: `True`, required. "
        },
        "star_logs": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "exists": true,
          "description": "Paths to the STAR log files (most frequently called Log.final.out)\n",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"Log.final.out\"]`. "
        },
        "gene_summary_logs": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "exists": true,
          "description": "Paths to the Summary.csv files from the STAR Solo output",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"Summary.txt\"]`. "
        },
        "reads_per_gene_logs": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "exists": true,
          "description": "Paths to the 'ReadsPerGene.out.tab' files as output by STAR.\n",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`. "
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "Tab-delimited file describing for each barcode (as the rows), the metrics (as columns)\ngathered from the different input files",
          "help_text": "Type: `file`, multiple: `False`, default: `\"starLogs.txt\"`, direction: `output`. ",
          "default": "starLogs.txt"
        }
      }
    },
    "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"
    }
  ]
}
