{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "split_modalities",
  "description": "Split the modalities from a single .h5mu multimodal sample into seperate .h5mu files. \n",
  "type": "object",
  "$defs": {
    "Dataset input": {
      "title": "Dataset input",
      "type": "object",
      "description": "Dataset input using nf-tower \"dataset\" or \"data explorer\". Allows for the input of multiple         parameter sets to initialise a Nextflow channel.",
      "properties": {
        "param_list": {
          "description": "Dataset input can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml                 blob. The names of the input fields (e.g. csv columns, json keys) need to be an exact match with the workflow input parameters.",
          "type": "string",
          "default": "",
          "format": "file-path",
          "mimetype": "text/csv"
        }
      }
    },
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Path to a single .h5mu file.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"sample_path\"`, direction: `input`. ",
          "default": "sample_path"
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output directory containing multiple h5mu files.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`, example: `\"/path/to/output\"`. ",
          "default": "$id.$key.output"
        },
        "output_types": {
          "type": "string",
          "format": "path",
          "description": "A csv containing the base filename and modality type per output file.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output_types.csv\"`, direction: `output`, example: `\"types.csv\"`. ",
          "default": "$id.$key.output_types.csv"
        },
        "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"
    }
  ]
}
