{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "cellranger_postprocessing",
  "description": "Post-processing Cell Ranger datasets.",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "id": {
          "type": "string",
          "description": "ID of the sample.",
          "help_text": "Type: `string`, multiple: `False`, required, example: `\"foo\"`. "
        },
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Input h5mu file created by running Cell Ranger and converting its output to h5mu.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.h5mu\"`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "The converted h5mu file.",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output\"`, direction: `output`. ",
          "default": "$id.$key.output"
        }
      }
    },
    "correction arguments": {
      "title": "Correction arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "perform_correction": {
          "type": "boolean",
          "description": "Whether or not to run CellBender to perform count correction.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "cellbender_epochs": {
          "type": "integer",
          "description": "Number of epochs to run CellBender for.",
          "help_text": "Type: `integer`, multiple: `False`, default: `150`. ",
          "default": 150
        }
      }
    },
    "filtering arguments": {
      "title": "Filtering arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "min_genes": {
          "type": "integer",
          "description": "Minimum number of counts required for a cell to pass filtering.",
          "help_text": "Type: `integer`, multiple: `False`, example: `100`. "
        },
        "min_counts": {
          "type": "integer",
          "description": "Minimum number of genes expressed required for a cell to pass filtering.",
          "help_text": "Type: `integer`, multiple: `False`, example: `1000`. "
        }
      }
    },
    "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/inputs"
    },
    {
      "$ref": "#/$defs/outputs"
    },
    {
      "$ref": "#/$defs/correction arguments"
    },
    {
      "$ref": "#/$defs/filtering arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
