nextflow_schema.json

{
  "$schema": "http://json-schema.org/draft-07/schema",
  "$id": "https://raw.githubusercontent.com/ont-tools/master/nextflow_schema.json",
  "title": "ont-tools pipeline parameters",
  "description": "ONT pipeline for reads QC and mapping.",
  "type": "object",
  "definitions": {
    "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": {
        "workflow": {
          "type": "string",
          "description": "Type of analysis to be run",
          "enum": [
            "concatenate",
            "reads-qc",
            "reads-filter",
            "chloroplast-contamination",
            "genome-mapping",
	    "genome-mapping-large",
            "isoform-analysis"
          ]
        },
        "help": {
          "type": "boolean",
          "description": "Display help text.",
          "fa_icon": "fas fa-question-circle",
          "hidden": true
        },
        "max_cpus": {
          "type": "integer",
          "hidden": true,
          "default": 8,
          "description": "Maximum number of cpus to use"
        },
        "max_memory": {
          "type": "string",
          "description": "Maximum memory to use",
          "default": "2.GB",
          "hidden": true
        }
      }
    },
    "input_output": {
      "title": "Input/output",
      "type": "object",
      "description": "Parameters for input/output directories",
      "default": "",
      "properties": {
        "input_dir": {
          "type": "string",
          "description": "Input directory containing samples to process"
        },
        "output_dir": {
          "type": "string",
          "description": "Output directory where the results will be written"
        }
      }
    },
    "reference_genomes": {
      "title": "Reference genomes",
      "type": "object",
      "description": "Files containing reference files for analysis",
      "default": "",
      "properties": {
        "genome_chl": {
          "type": "string",
          "description": "Chloroplast genome (small file)"
        },
        "genome_nuc": {
          "type": "string",
          "description": "Nuclear genome"
        },
        "genes": {
          "type": "string",
          "description": "Genes in gtf format",
          "pattern": ".gtf",
          "format": "file-path"
        }
      }
    },
    "filtering_parameters": {
      "title": "Filtering parameters",
      "type": "object",
      "description": "Reads features used for filtering",
      "default": "",
      "properties": {
        "phred_score": {
          "type": "integer",
          "description": "Phres score used to exclude reads",
          "default": 7
        }
      }
    },
    "institutional_config_options": {
      "title": "Institutional config options",
      "type": "object",
      "fa_icon": "fas fa-university",
      "description": "Parameters used to describe centralised config profiles. These should not be edited.",
      "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
      "properties": {
        "custom_config_base": {
          "type": "string",
          "description": "Base directory for Institutional configs.",
          "default": ".",
          "hidden": true,
          "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
          "fa_icon": "fas fa-users-cog"
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/definitions/generic_options"
    },
    {
      "$ref": "#/definitions/input_output"
    },
    {
      "$ref": "#/definitions/reference_genomes"
    },
    {
      "$ref": "#/definitions/filtering_parameters"
    },
    {
      "$ref": "#/definitions/institutional_config_options"
    }
  ]
}