{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "generate_well_statistics",
  "description": "Generate summary statistics from BAM files generated by STAR solo.",
  "type": "object",
  "$defs": {
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "description": "The .bam file as returned by the mapping tool STAR.",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"input.bam\"`. "
        },
        "barcode": {
          "type": "string",
          "description": "The barcode for the well that is being processed",
          "help_text": "Type: `string`, multiple: `False`, required. "
        },
        "well_id": {
          "type": "string",
          "description": "ID of this well",
          "help_text": "Type: `string`, multiple: `False`, required. "
        },
        "processedBAMFile": {
          "type": "string",
          "format": "path",
          "description": "Path to a .tsv file listing, per read in the BAM file,\nthe value for the \"CB\", \"UX\", \"GX\" and \"GN\" tag, together with the\nchromsome to which the read was mapped to.\n",
          "help_text": "Type: `file`, multiple: `False`, default: `\"processedBamFile.txt\"`, direction: `output`. ",
          "default": "processedBamFile.txt"
        },
        "nrReadsNrGenesPerChrom": {
          "type": "string",
          "format": "path",
          "description": "Path to an output file that contains a .tsv formatted table describing\nper chromosome the number of reads that were mapped to that chromosome (NumberOfReads\ncolumn) and the number of genes on that chromosome that had at least one\nread mapped to it (NumberOfGenes).\n",
          "help_text": "Type: `file`, multiple: `False`, default: `\"nrReadsNrGenesPerChrom.txt\"`, direction: `output`. ",
          "default": "nrReadsNrGenesPerChrom.txt"
        },
        "nrReadsNrUMIsPerCB": {
          "type": "string",
          "format": "path",
          "description": "Path to an output file that contains a .tsv formatted table describing\nper barcode the number of UMI's (nrUMIs) and the total number of reads (NumberOfReads).\n",
          "help_text": "Type: `file`, multiple: `False`, default: `\"nrReadsNrUMIsPerCB.txt\"`, direction: `output`. ",
          "default": "nrReadsNrUMIsPerCB.txt"
        },
        "umiFreqTop": {
          "type": "string",
          "format": "path",
          "description": "Path to an output file that contains a .tsv formatted table describing\nper UMI (column UB) the frequency at which they occur in the reads (column\nN)",
          "help_text": "Type: `file`, multiple: `False`, default: `\"umiFreqTop100.txt\"`, direction: `output`. ",
          "default": "umiFreqTop100.txt"
        },
        "threads": {
          "type": "integer",
          "description": "Number of threads to use for decompressing BAM files.\n",
          "help_text": "Type: `integer`, multiple: `False`, default: `1`. ",
          "default": 1
        }
      }
    },
    "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"
    }
  ]
}
