nextflow_schema.json

{
  "$schema": "http://json-schema.org/draft-07/schema",
  "$id": "https://raw.githubusercontent.com/ajandria/futuriandge/master/nextflow_schema.json",
  "title": "ajandria/futuriandge pipeline parameters",
  "description": "RNA-seq pipeline for differential gene expression analysis (specfic to MUB infrastructure)",
  "type": "object",
  "definitions": {
    "mub_s_reference_files": {
      "title": "MUB's Reference Files",
      "type": "object",
      "description": "References used for up-stream analyses",
      "default": "",
      "properties": {
        "organism": {
          "type": "string",
          "description": "Required organism"
        },
        "reference_genome": {
          "type": "string",
          "default": "default hardcoded",
          "hidden": true,
          "description": "Hardcoded depending on params.organism"
        },
        "gtf": {
          "type": "string",
          "default": "default hardcoded",
          "hidden": true,
          "description": "Hardcoded depending on params.organism"
        },
        "refFlat": {
          "type": "string",
          "default": "default hardcoded",
          "hidden": true,
          "description": "Hardcoded depending on params.organism"
        },
        "salmon_index": {
          "type": "string",
          "default": "default hardcoded",
          "hidden": true,
          "description": "Hardcoded depending on params.organism"
        },
        "gene_map": {
          "type": "string",
          "default": "default hardcoded",
          "hidden": true,
          "description": "Hardcoded depending on params.organism"
        },
        "rRNA_db_path": {
          "type": "string",
          "default": "default hardcoded",
          "description": "Path to SILVA db for SortMeRNA",
          "hidden": true
        }
      },
      "required": [
        "organism",
        "reference_genome",
        "gtf",
        "refFlat",
        "salmon_index",
        "gene_map",
        "rRNA_db_path"
      ]
    },
    "general_setup": {
      "title": "General setup",
      "type": "object",
      "description": "MUB's parameters",
      "default": "",
      "properties": {
        "input": {
          "type": "string",
          "default": "${baseDir}/tests/test_sample_sheet.csv"
        },
        "outDir": {
          "type": "string",
          "default": "${baseDir}/results",
          "description": "Output directory"
        },
        "contrasts": {
          "type": "string",
          "description": "If missing the downstream subworkflow won't run",
          "format": "path"
        }
      },
      "required": ["input"]
    },
    "additional_run_specific_parameters": {
      "title": "Additional Run-Specific Parameters",
      "type": "object",
      "description": "",
      "default": "",
      "properties": {
        "schema_ignore_params": {
          "type": "string",
          "default": "genomes"
        },
        "monochrome_logs": {
          "type": "boolean",
          "hidden": true,
          "description": "Print help and logs in monochrome"
        },
        "validate_params": {
          "type": "boolean",
          "default": true,
          "hidden": true,
          "description": "Whether to validate parameters"
        },
        "show_hidden_params": {
          "type": "boolean",
          "hidden": true,
          "description": "Whether to show hidden parameters"
        },
        "help": {
          "type": "boolean",
          "hidden": true,
          "description": "Whether to show help msg"
        },
        "max_time": {
          "type": "string",
          "description": "Max working time",
          "hidden": true,
          "default": "240.h"
        },
        "max_memory": {
          "type": "string",
          "hidden": true,
          "description": "Max memory used",
          "default": "16.GB"
        },
        "max_cpus": {
          "type": "number",
          "description": "Max no of CPUs",
          "hidden": true,
          "default": 48
        },
        "config_profile_description": {
          "type": "string",
          "description": "Description of custom profile",
          "default": "Using global options for standard run"
        },
        "config_profile_name": {
          "type": "string",
          "description": "Name of a custom profile",
          "default": "Global"
        },
        "version": {
          "type": "string",
          "default": "false",
          "hidden": true
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/definitions/mub_s_reference_files"
    },
    {
      "$ref": "#/definitions/general_setup"
    },
    {
      "$ref": "#/definitions/additional_run_specific_parameters"
    }
  ]
}