import_large_geojson/nextflow_schema.json at main · BioimageAnalysisCoreWEHI/import_large_geojson · GitHub

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{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://raw.githubusercontent.com/BioimageAnalysisCoreWEHI/import_large_geojson/main/nextflow_schema.json",
  "title": "import_large_geojson pipeline parameters",
  "description": "Headless QuPath import of large GeoJSON cell annotations into a QuPath project",
  "type": "object",
  "$defs": {
    "input_output_options": {
      "title": "Input/output options",
      "type": "object",
      "required": ["project", "geojson_dir"],
      "properties": {
        "project": {
          "type": "string",
          "format": "file-path",
          "exists": true,
          "description": "Path to QuPath project .qpproj file"
        },
        "qupath_bin": {
          "type": "string",
          "format": "file-path",
          "exists": true,
          "default": "/stornext/System/data/software/rhel/9/base/tools/QuPath/0.6.0/bin/QuPath",
          "description": "Path to QuPath executable"
        },
        "script": {
          "type": "string",
          "format": "file-path",
          "exists": true,
          "default": "bin/import_large_geojson.groovy",
          "description": "Path to Groovy script run by QuPath in headless mode"
        },
        "geojson_dir": {
          "type": "string",
          "format": "directory-path",
          "exists": true,
          "description": "Directory containing GeoJSON files to import. Files are matched to QuPath images by name."
        },
        "clear_existing": {
          "type": "boolean",
          "default": true,
          "description": "Clear all existing objects from each image before importing new GeoJSON objects"
        },
        "file_pattern": {
          "type": "string",
          "default": "{stem}.geojson",
          "description": "Filename pattern for matching GeoJSON files to images. {stem} is replaced with the image name (without extension)."
        },
        "outdir": {
          "type": "string",
          "format": "directory-path",
          "description": "Output directory for log files"
        },
        "publish_dir_mode": {
          "type": "string",
          "default": "copy",
          "description": "Method used by Nextflow publishDir",
          "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"]
        },
        "resolve_hierarchy": {
          "type": "boolean",
          "default": true,
          "description": "Run QuPath resolveHierarchy() after import. Set false for flat detections to skip O(n^2) nesting step."
        }
      }
    },
    "generic_options": {
      "title": "Generic options",
      "type": "object",
      "properties": {
        "validate_params": {
          "type": "boolean",
          "default": true,
          "hidden": true,
          "description": "Validate parameters against schema"
        }
      }
    }
  },
  "allOf": [
    { "$ref": "#/$defs/input_output_options" },
    { "$ref": "#/$defs/generic_options" }
  ]
}