{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "bcl_convert",
  "description": "Convert bcl files to fastq files using bcl-convert.\nInformation about upgrading from bcl2fastq via\nhttps://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html\nand https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html\n",
  "type": "object",
  "$defs": {
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input run directory",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"bcl_dir\"`. "
        },
        "sample_sheet": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Pointer to the sample sheet",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"bcl_dir\"`. "
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output directory containig fastq files",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`, example: `\"fastq_dir\"`. ",
          "default": "$id.$key.output"
        },
        "reports": {
          "type": "string",
          "format": "path",
          "description": "Reports directory",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.reports\"`, direction: `output`, example: `\"reports_dir\"`. ",
          "default": "$id.$key.reports"
        },
        "test_mode": {
          "type": "boolean",
          "description": "Should bcl-convert be run in test mode (using --first-tile-only)?",
          "help_text": "Type: `boolean`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "strict_mode": {
          "type": "boolean",
          "description": "Abort if any files are missing.",
          "help_text": "Type: `boolean`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "tiles": {
          "type": "string",
          "description": "Process only a subset of tiles by a regular expression.",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "exclude_tiles": {
          "type": "string",
          "description": "Exclude set of tiles by a regular expression",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "no_lane_splitting": {
          "type": "boolean",
          "description": "Wheter to avoid splitting FASTQ file by lane.",
          "help_text": "Type: `boolean`, multiple: `False`. "
        }
      }
    },
    "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"
    }
  ]
}
