{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "conversion",
  "description": "A pipeline to convert different file formats to .h5mu.",
  "type": "object",
  "$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": "Path to the sample.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.h5mu\"`. "
        },
        "input_type": {
          "type": "string",
          "description": "Type of the input file",
          "help_text": "Type: `string`, multiple: `False`, required, choices: ``10xmtx`, `10xh5`, `h5ad``. ",
          "enum": [
            "10xmtx",
            "10xh5",
            "h5ad"
          ]
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Name or template for the output files.",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        }
      }
    },
    "conversion from h5ad": {
      "title": "Conversion from h5ad",
      "type": "object",
      "description": "No description",
      "properties": {
        "modality": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "Name of the modality where the h5ad is stored in the h5mu object.",
          "help_text": "Type: `string`, multiple: `True`. "
        }
      }
    },
    "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/conversion from h5ad"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
