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.",
      "properties": {
        "email": {
          "type": "string",
          "description": "Email address for completion summary.",
          "fa_icon": "fas fa-envelope",
          "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
          "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
        }
      },
      "required": ["email"]
    },
    "generic_options": {
      "title": "Generic options",
      "type": "object",
      "fa_icon": "fas fa-file-import",
      "description": "Less common options for the pipeline, typically set in a config file.",
      "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
      "properties": {
        "help": {
          "type": "boolean",
          "description": "Display help text.",
          "fa_icon": "fas fa-question-circle",
          "hidden": true
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/definitions/input_output_options"
    },
    {
      "$ref": "#/definitions/generic_options"
    }
  ],
  "properties": {
    "event": {
      "type": "string",
      "default": "biotechx_basel_2024",
      "fa_icon": "far fa-calendar-alt",
      "description": "Which event are you participating in?",
      "hidden": true
    },
    "outdir": {
      "type": "string",
      "default": "results",
      "hidden": true
    },
    "ticket_number_emit_session_id": {
      "type": "boolean",
      "hidden": true
    }
  }
}