nextflow_schema.json

{
  "$schema": "http://json-schema.org/draft-07/schema",
  "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
  "title": ". pipeline parameters",
  "description": "",
  "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",
          "exists": true,
          "mimetype": "text/csv",
          "pattern": "^\\S+\\.csv$",
          "description": "Path to comma-separated file containing information about the samples in the experiment.",
          "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.",
          "fa_icon": "fas fa-file-csv"
        },
        "outdir": {
          "type": "string",
          "format": "directory-path",
          "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
          "fa_icon": "fas fa-folder-open",
          "help_text": ""
        }
      }
    },
    "pipeline_options": {
      "title": "Pipeline options",
      "type": "object",
      "description": "",
      "default": "",
      "properties": {
        "outsuffix": {
          "type": "string",
          "default": "_cleaned",
          "description": "Suffix for output files (default: _cleaned)"
        },
        "rm_svs_label": {
          "type": "boolean",
          "default": true,
          "description": "Boolean indicating whether to remove the label image in SVS files (default: true)"
        },
        "rm_svs_macro": {
          "type": "boolean",
          "description": "Boolean indicating whether to remove the macro image in SVS files (default: true)"
        },
        "rm_ome_sa": {
          "type": "boolean",
          "default": true,
          "description": "Boolean indicating whether to remove structural annotations in OME-XML files (default: true)"
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/definitions/input_output_options"
    },
    {
      "$ref": "#/definitions/pipeline_options"
    }
  ]
}