{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "cellranger_count_split",
  "description": "Split 10x Cell Ranger output directory into separate output fields.",
  "type": "object",
  "$defs": {
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Output directory from a Cell Ranger count run.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input_dir\"`. "
        },
        "filtered_h5": {
          "type": "string",
          "format": "path",
          "description": "Output path for the h5 file storing the filtered counts.\n",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.filtered_h5.h5\"`, direction: `output`, example: `\"filtered_feature_bc_matrix.h5\"`. ",
          "default": "$id.$key.filtered_h5.h5"
        },
        "metrics_summary": {
          "type": "string",
          "format": "path",
          "description": "Where to store the 'metrics_summary' CSV file.\n",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.metrics_summary.csv\"`, direction: `output`, example: `\"metrics_summary.csv\"`. ",
          "default": "$id.$key.metrics_summary.csv"
        },
        "molecule_info": {
          "type": "string",
          "format": "path",
          "description": "Where to store Cell Ranger's 'molecule_info.h5' file.\n",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.molecule_info.h5\"`, direction: `output`, example: `\"molecule_info.h5\"`. ",
          "default": "$id.$key.molecule_info.h5"
        },
        "bam": {
          "type": "string",
          "format": "path",
          "description": "Location of output BAM files.\n",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.bam.bam\"`, direction: `output`, example: `\"possorted_genome_bam.bam\"`. ",
          "default": "$id.$key.bam.bam"
        },
        "bai": {
          "type": "string",
          "format": "path",
          "description": "Where to store the BAM index files.\n",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.bai.bai\"`, direction: `output`, example: `\"possorted_genome_bam.bam.bai\"`. ",
          "default": "$id.$key.bai.bai"
        },
        "raw_h5": {
          "type": "string",
          "format": "path",
          "description": "Output path for the h5 file storing the raw counts.\n",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.raw_h5.h5\"`, direction: `output`, example: `\"raw_feature_bc_matrix.h5\"`. ",
          "default": "$id.$key.raw_h5.h5"
        }
      }
    },
    "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"
    }
  ]
}
