nextflow_schema.json

{
  "$schema": "http://json-schema.org/draft-07/schema",
  "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
  "title": ". pipeline parameters",
  "description": "NextFlow pipeline to run HistoQC",
  "type": "object",
  "definitions": {
    "input_output_options": {
      "title": "Input/output options",
      "type": "object",
      "fa_icon": "fas fa-terminal",
      "description": "Define where the pipeline should find input data and save output data.",
      "required": ["input", "outdir"],
      "properties": {
        "input": {
          "type": "string",
          "format": "file-path",
          "mimetype": "text/csv",
          "description": "Path to a CSV samplesheet"
        },
        "outDir": {
          "type": "string",
          "description": "Directory in which outputs are placed",
          "default": "outputs"
        }
      }
    },
    "HistoQC options": {
      "title": "HistoQC options",
      "type": "object",
      "fa_icon": "fas fa-solid fa-microscope",
      "description": "Define parameters for HistoQC",
      "required": ["config"],
      "properties": {
        "config": {
          "type": "string",
          "default": "default",
          "enum": ["default", "ihc", "clinical", "first", "light", "v2.1"],
          "description": "Name of built-in HistoQC config. Overridden by `custom_config`."
        },
        "custom_config": {
          "type": "string",
          "format": "file-path",
          "mimetype": "text/plain",
          "description": "Path to a HistoQC config `.ini` file. Overrides `config`"
        },
        "group": {
          "title": "Output grouping",
          "type": "boolean",
          "description": "Arrange outputs into subfolders defined by the samplesheet `group` column"
        }
      }
    },
    "conversion_options": {
      "title": "Conversion options",
      "type": "object",
      "fa_icon": "fas fa-solid fa-magic",
      "description": "Define parameters used during conversion to openslide compatible tiff",
      "properties": {
        "convert": {
            "type": "boolean",
            "description": "Should images be converted to an openslide compatible tiff",
            "hidden": true
        },
        "mag": {
            "type": "integer",
            "description": "Nominal magnification to inject into openslide compatible tiff",
            "hidden": true
        },
        "mpp": {
          "type": "number",
          "description": "Image resolution (microns per pixel) to inject into openslide compatible tiff",
          "hidden": true
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/definitions/input_parameters"
    }
  ]
}