nextflow_schema.json

{
  "$schema": "http://json-schema.org/draft-07/schema",
  "$id": "https://raw.githubusercontent.com/polio-nanopore/piranha/main/nextflow_schema.json",
  "title": "polio-nanopore/piranha",
  "description": "Polio investigation resource automating nanopore haplotype analysis.",
  "url": "https://github.com/polio-nanopore/piranha",
  "demo_url": "https://raw.githubusercontent.com/polio-nanopore/piranha/main/demo.tar.gz",
  "type": "object",
  "definitions": {
    "input_options": {
      "title": "Input Options",
      "type": "object",
      "fa_icon": "fas fa-terminal",
      "description": "Define where the pipeline should find input data and save output data.",
      "properties": {
        "barcodes_csv": {
          "type": "string",
          "format": "file-path",
          "title": "Barcodes",
          "description": "A CSV file with barcode and sample columns.",
          "help_text": ".",
          "demo_data": "barcodes01.csv"
        },
        "run_dir": {
          "type": "string",
          "format": "directory-path",
          "title": "Run directory",
          "description": "A directory containing a directory of fastq for a each barcode in a run.",
          "help_text": "A directory containing subdirectories of fastq files as created by MinKNOW.",
          "demo_data": "demultiplexed"
        }
      },
      "allOf": [
        {
          "required": [
            "barcodes_csv",
            "run_dir"
          ]
        }
      ]
    },
    "output_options": {
      "title": "Output Options",
      "type": "object",
      "fa_icon": "fas fa-terminal",
      "description": "Parameters for saving and naming workflow outputs.",
      "properties": {
        "out_dir": {
          "type": "string",
          "format": "directory-path",
          "default": "output",
          "title": "Output folder name",
          "description": "Directory for output of all user-facing files."
        },
        "output_intermediates": {
          "type": "boolean",
          "title": "Output intermediate files"
        }
      }
    },
    "analysis_options": {
      "title": "Analysis Options",
      "type": "object",
      "fa_icon": "fas fa-terminal",
      "description": "Define the thresholds for filtering and assembly.",
      "properties": {
        "config": {
          "type": "string",
          "format": "file-path",
          "title": "Config file",
          "description": "A config file with parameters for piranha."
        },
        "min_map_quality": {
          "type": "integer",
          "title": "Minimum mapping quality"
        },
        "min_read_length": {
          "type": "integer",
          "title": "Minimum read length"
        },
        "max_read_length": {
          "type": "integer",
          "title": "Maximum read length"
        },
        "min_read_depth": {
          "type": "integer",
          "title": "Minimum read depth required for consensus generation"
        },
        "min_read_pcent": {
          "type": "number",
          "title": "Minimum percentage of sample required for consensus generation"
        },
        "primer_length": {
          "type": "integer",
          "title": "Length of primer sequences to trim off start and end of reads"
        }
      }
    },
    "phylo_options": {
      "title": "Phylogenetic Options",
      "type": "object",
      "description": "Options for running the phylogenetics module.",
      "properties": {
        "run_phylo": {
          "type": "boolean",
          "title": "Run phylogenetics pipeline"
        },
        "supplementary_datadir": {
          "type": "string",
          "format": "path",
          "title": "Supplementary data",
          "description": "Path to directory containing supplementary sequence FASTA file and optional metadata to be incorporated into phylogenetic analysis."
        }
      }
    },
    "miscellaneous_options": {
      "title": "Miscellaneous Options",
      "type": "object",
      "fa_icon": "fas fa-file-import",
      "description": "Everything else.",
      "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",
          "title": "Display help text",
          "fa_icon": "fas fa-question-circle",
          "hidden": true
        },
        "version": {
          "type": "boolean",
          "title": "Display version",
          "description": "Display version and exit.",
          "fa_icon": "fas fa-question-circle",
          "hidden": true
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/definitions/input_options"
    },
    {
      "$ref": "#/definitions/output_options"
    },
    {
      "$ref": "#/definitions/analysis_options"
    },
    {
      "$ref": "#/definitions/phylo_options"
    },
    {
      "$ref": "#/definitions/miscellaneous_options"
    }
  ],
  "properties": {
    "aws_image_prefix": {
      "type": "string",
      "title": "AWS image prefix",
      "hidden": true
    },
    "aws_queue": {
      "type": "string",
      "title": "AWS queue",
      "hidden": true
    },
    "monochrome_logs": {
      "type": "boolean"
    },
    "validate_params": {
      "type": "boolean",
      "default": true
    },
    "show_hidden_params": {
      "type": "boolean"
    }
  },
  "docs": {
    "intro": "\n## Introduction\n\nPiranha blah.\n\n",
    "links": "## Useful links\n\n* [nextflow](https://www.nextflow.io/)\n* [docker](https://www.docker.com/products/docker-desktop)"
  }
}