{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "add_id",
  "description": "Add id of .obs. Also allows to make .obs_names (the .obs index) unique \nby prefixing the values with an unique id per .h5mu file.\n",
  "type": "object",
  "$defs": {
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Path to the input .h5mu.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"sample_path\"`. "
        },
        "input_id": {
          "type": "string",
          "description": "The input id.",
          "help_text": "Type: `string`, multiple: `False`, required. "
        },
        "obs_output": {
          "type": "string",
          "description": "Name of the .obs column where to store the id.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"sample_id\"`. ",
          "default": "sample_id"
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "Name of output MuData file.\n",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        },
        "make_observation_keys_unique": {
          "type": "boolean",
          "description": "Join the id to the .obs index (.obs_names).",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "output_compression": {
          "type": "string",
          "description": "Compression format to use for the output AnnData and/or Mudata objects.\nBy default no compression is applied.\n",
          "help_text": "Type: `string`, multiple: `False`, example: `\"gzip\"`, choices: ``gzip`, `lzf``. ",
          "enum": [
            "gzip",
            "lzf"
          ]
        }
      }
    },
    "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"
    }
  ]
}
