{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "cellranger_count",
  "description": "Count gene expression and/or feature barcode reads from a single sample and GEM well\n",
  "type": "object",
  "$defs": {
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "The folder to store the alignment results.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ",
          "default": "$id.$key.output"
        },
        "create_bam": {
          "type": "boolean",
          "description": "Enable or disable BAM file generation",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "no_secondary": {
          "type": "boolean",
          "description": "Disable secondary analysis, e.g",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        }
      }
    },
    "fastq inputs": {
      "title": "FASTQ inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "fastqs": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "exists": true,
          "description": "The fastq.gz files to align",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"sample_S1_L001_R1_001.fastq.gz\";\"sample_S1_L001_R2_001.fastq.gz\"]`. "
        },
        "description": {
          "type": "string",
          "description": "Sample description to embed in output files",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "sample": {
          "type": "string",
          "description": "Prefix of the filenames of FASTQs to select",
          "help_text": "Type: `string`, multiple: `False`, example: `\"sample_S1\"`. "
        },
        "lanes": {
          "type": "array",
          "items": {
            "type": "integer"
          },
          "description": "Only use FASTQs from selected lanes.",
          "help_text": "Type: `integer`, multiple: `True`, example: `[1;2;3]`. "
        },
        "libraries": {
          "type": "string",
          "format": "path",
          "description": "CSV file declaring input library data sources",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"libraries.csv\"`. "
        }
      }
    },
    "reference inputs": {
      "title": "Reference inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "transcriptome": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Path of folder containing 10x-compatible transcriptome reference",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"transcriptome.tar.gz\"`. "
        },
        "feature_ref": {
          "type": "string",
          "format": "path",
          "description": "Feature reference CSV file, declaring Feature Barcode constructs and associated barcodes",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"feature_ref.csv\"`. "
        }
      }
    },
    "analysis settings": {
      "title": "Analysis settings",
      "type": "object",
      "description": "No description",
      "properties": {
        "expect_cells": {
          "type": "integer",
          "description": "Expected number of recovered cells, used as input to cell calling algorithm.",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "force_cells": {
          "type": "integer",
          "description": "Force pipeline to use this number of cells, bypassing cell calling algorithm",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "r1_length": {
          "type": "integer",
          "description": "Hard trim the input Read 1 to this length before analysis",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "r2_length": {
          "type": "integer",
          "description": "Hard trim the input Read 2 to this length before analysis",
          "help_text": "Type: `integer`, multiple: `False`. "
        },
        "include_introns": {
          "type": "boolean",
          "description": "Include intronic reads in count",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "chemistry": {
          "type": "string",
          "description": "Assay configuration.\n\nNOTE: by default the assay configuration is detected automatically, which is the recommended mode",
          "help_text": "Type: `string`, multiple: `False`, example: `\"auto\"`. "
        },
        "cell_annotation_model": {
          "type": "string",
          "description": "Cell annotation model to use",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "min_crispr_umi": {
          "type": "integer",
          "description": "Minimum CRISPR UMI threshold",
          "help_text": "Type: `integer`, multiple: `False`. "
        }
      }
    },
    "additional arguments": {
      "title": "Additional arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "no_libraries": {
          "type": "boolean",
          "description": "Proceed with processing using a `--feature_ref` but no Feature Barcode libraries specified with the 'libraries' flag.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "check_library_compatibility": {
          "type": "boolean",
          "description": "Whether to check for barcode compatibility between libraries.\n",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "tenx_cloud_token": {
          "type": "string",
          "format": "path",
          "description": "The path to the 10x Cloud Analysis user token used to enable cell\nannotation",
          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
        },
        "dry": {
          "type": "boolean",
          "description": "Do not execute the pipeline",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": 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/outputs"
    },
    {
      "$ref": "#/$defs/fastq inputs"
    },
    {
      "$ref": "#/$defs/reference inputs"
    },
    {
      "$ref": "#/$defs/analysis settings"
    },
    {
      "$ref": "#/$defs/additional arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
