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

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{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://raw.githubusercontent.com/BioimageAnalysisCoreWEHI/opal_inform_stitch/main/nextflow_schema.json",
  "title": "opal_inform_stitch pipeline parameters",
  "description": "Nextflow pipeline for stitching Opal/inForm images from Vectra Polaris in parallel",
  "type": "object",
  "$defs": {
    "input_output_options": {
      "title": "Input/output options",
      "type": "object",
      "required": ["base_dir", "outdir"],
      "properties": {
        "base_dir": {
          "type": "string",
          "format": "directory-path",
          "exists": true,
          "description": "Base directory containing one subdirectory per slide/sample. Each subdirectory must contain component_data TIFF tiles from inForm."
        },
        "outdir": {
          "type": "string",
          "format": "directory-path",
          "description": "Output directory for stitched OME-TIFF files."
        },
        "publish_dir_mode": {
          "type": "string",
          "default": "copy",
          "description": "Method used by Nextflow publishDir to stage output files.",
          "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"]
        }
      }
    },
    "roi_finder_options": {
      "title": "ROI finder options",
      "type": "object",
      "properties": {
        "roi_finder": {
          "type": "boolean",
          "default": false,
          "description": "Detect individual tissue regions and write one OME-TIFF per ROI instead of a single stitched image. Useful when a slide contains multiple spatially separated tissue sections."
        },
        "roi_scale": {
          "type": "integer",
          "default": 8,
          "minimum": 1,
          "description": "Downscale factor for the occupancy map used in ROI detection. Higher values are faster but may merge nearby tissue sections."
        }
      }
    },
    "generic_options": {
      "title": "Generic options",
      "type": "object",
      "properties": {
        "help": {
          "type": "boolean",
          "default": false,
          "description": "Display help text.",
          "hidden": true
        },
        "version": {
          "type": "boolean",
          "default": false,
          "description": "Display version and exit.",
          "hidden": true
        },
        "monochrome_logs": {
          "type": "boolean",
          "default": false,
          "description": "Do not use coloured log outputs.",
          "hidden": true
        }
      }
    }
  },
  "allOf": [
    { "$ref": "#/$defs/input_output_options" },
    { "$ref": "#/$defs/roi_finder_options" },
    { "$ref": "#/$defs/generic_options" }
  ]
}