{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "$id": "https://schema.humancellatlas.org/type/file/8.0.0/analysis_file",
  "description": "A file analysis results produced by a secondary analysis pipeline.",
  "additionalProperties": false,
  "required": [
    "describedBy",
    "schema_type",
    "file_core",
    "genome_assembly_version",
    "alignment_software"
  ],
  "title": "Analysis file",
  "name": "analysis_file",
  "type": "object",
  "properties": {
    "describedBy": {
      "description": "The URL reference to the schema.",
      "type": "string",
      "pattern": "^(http|https)://schema.(.*?)humancellatlas.org/type/file/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/analysis_file"
    },
    "schema_version": {
      "description": "The version number of the schema in major.minor.patch format.",
      "type": "string",
      "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$",
      "example": "4.6.1"
    },
    "schema_type": {
      "description": "The type of the metadata schema entity.",
      "type": "string",
      "enum": [
        "file"
      ]
    },
    "provenance": {
      "description": "Provenance information provided by the system.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/system/1.1.0/provenance"
    },
    "file_core": {
      "description": "Core file-level information.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/core/file/6.4.0/file_core",
      "user_friendly": "File core"
    },
    "matrix_cell_count": {
      "description": "Number of cells analyzed in a matrix file.",
      "type": "integer",
      "maximum": 1000000000,
      "minimum": 0,
      "example": "1; 2100",
      "user_friendly": "Matrix cell count",
      "guidelines": "If the analysis file is a matrix containing cells, enter the exact number of cells in the matrix."
    },
    "genome_assembly_version": {
      "description": "Name of the genome assembly used to generate this file.",
      "type": "string",
      "user_friendly": "Genome version",
      "enum": [
        "GRCh38",
        "GRCh37",
        "GRCm39",
        "GRCm38",
        "GRCm37",
        "Not Applicable"
      ],
      "guidelines": "Please use the name as defined in the Genome Reference Consortium (https://www.ncbi.nlm.nih.gov/grc)",
      "example": "Should be one of: GRCh38, GRCh37, GRCm39, GRCm38, GRCm37, Not Applicable"
    },
    "genome_patch_version": {
      "description": "Patch version of the genome assembly used to generate this file.",
      "type": "string",
      "user_friendly": "Patch version",
      "example": "p11; p14"
    },
    "alignment_software": {
      "description": "Name of alignment software used to map FASTQ files to reference genome",
      "type": "string",
      "user_friendly": "Alignment software",
      "example": "Cellranger; kallisto bustools; GSNAP; STAR"
    },
    "alignment_software_version": {
      "description": "Version of alignment software used to map FASTQ files to reference genome",
      "type": "string",
      "user_friendly": "Alignment software",
      "pattern": "^v{0,}[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$",
      "example": "v2.0.1; 2.4.2a; v0.45.2"
    }
  }
}