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

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{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://raw.githubusercontent.com/BioimageAnalysisCoreWEHI/prepare_celltune_features/main/nextflow_schema.json",
  "title": "prepare_celltune_features pipeline parameters",
  "description": "Extract cell measurements from QuPath geojson.gz files and format for CellTune import",
  "type": "object",
  "$defs": {
    "input_output_options": {
      "title": "Input/output options",
      "type": "object",
      "required": ["geojson_dir", "pixel_size", "outdir"],
      "properties": {
        "geojson_dir": {
          "type": "string",
          "format": "directory-path",
          "exists": true,
          "description": "Directory containing *.geojson.gz files from QuPath cell measurements"
        },
        "pixel_size": {
          "type": "number",
          "exclusiveMinimum": 0,
          "description": "Pixel size in µm/pixel for centroid conversion (e.g. 0.3906 for MIBI, 0.4 for COMET)"
        },
        "cofactor": {
          "type": "number",
          "default": 100,
          "exclusiveMinimum": 0,
          "description": "Cofactor for arcsinh normalization. 100 for MIBI/IMC, 0.1 for fluorescence (CODEX/COMET)"
        },
        "skip_arcsinh": {
          "type": "boolean",
          "default": false,
          "description": "Skip arcsinh normalization and output raw measurements"
        },
        "mask_suffix": {
          "type": "string",
          "default": "_mask.tiff",
          "description": "Suffix of mask files to rename to _segmentation_labels.tif for CellTune"
        },
        "output": {
          "type": "string",
          "default": "celltune_features.parquet",
          "description": "Output parquet file name"
        },
        "celltune_cell_table": {
          "type": "string",
          "format": "file-path",
          "exists": true,
          "description": "Optional path to CellTune cellTable_region_props.parquet. When provided, cells absent from the reference are removed from the output and recorded in dropped_cells.csv."
        },
        "outdir": {
          "type": "string",
          "format": "directory-path",
          "description": "Output directory for published files"
        },
        "publish_dir_mode": {
          "type": "string",
          "default": "copy",
          "description": "Method used by Nextflow publishDir",
          "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"]
        }
      }
    },
    "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" }
  ]
}