{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "cellranger_atac_mkfastq",
  "description": "Demultiplex raw sequencing data for ATAC experiments",
  "type": "object",
  "$defs": {
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Path of Illumina BCL run folder.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"/path/to/bcl\"`. "
        },
        "csv": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "The path to the simple layout sample sheet.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"SampleSheet.csv\"`. "
        },
        "lanes": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "bcl2fastq option",
          "help_text": "Type: `string`, multiple: `True`, example: `[\"1,3\"]`. "
        },
        "use_bases_mask": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "bcl2fastq option",
          "help_text": "Type: `string`, multiple: `True`, example: `[\"y50n,I6n,Y50n\"]`. "
        },
        "delete_undetermined": {
          "type": "boolean",
          "description": "bcl2fastq option",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "barcode_mismatches": {
          "type": "integer",
          "description": "bcl2fastq option",
          "help_text": "Type: `integer`, multiple: `False`, default: `1`. ",
          "default": 1
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "The folder to store the demux results",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"fastqs\"`, direction: `output`, example: `\"/path/to/output\"`. ",
          "default": "fastqs"
        },
        "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"
        }
      }
    },
    "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"
    }
  ]
}
