nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/isPCR/master/nextflow_schema.json",
    "title": "isPCR pipeline parameters",
    "description": "Rapid local alignment search using in-silico PCR",
    "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"
            ],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "schema": "assets/schema_input.json",
                    "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. See [usage docs](https://nf-co.re//usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "outdir": {
                    "type": "string",
                    "description": "Path to the output directory where the results will be saved.",
                    "default": "./results",
                    "fa_icon": "fas fa-folder-open",
                    "format": "directory-path"
                },
                "input_format": {
                    "type": "string",
                    "default": "fasta",
                    "description": "Format of input sequences (fasta|fastq)",
                    "enum": [
                        "fasta",
                        "fastq"
                    ],
                    "fa_icon": "fas fa-info-circle"
                }
            }
        },
        "pcr_parameters": {
            "title": "PCR parameters",
            "type": "object",
            "fa_icon": "fas fa-tasks",
            "properties": {
                "primer": {
                    "type": "string",
                    "default": "None",
                    "format": "file-path",
                    "description": "Path to primer sequence(s)"
                },
                "max_length": {
                    "type": "integer",
                    "default": 1000,
                    "description": "Maximum length of target amplicon"
                },
                "probe_min_tm": {
                    "type": "integer",
                    "default": 40,
                    "description": "Minimum probe hybridization melting temperature required in Celsius"
                },
                "primer_min_tm": {
                    "type": "integer",
                    "default": 40,
                    "description": "Minimum primer hybridization melting temperature required in Celsius"
                },
                "multiplex": {
                    "type": "boolean",
                    "description": "Run all primer/probe pairs in a single assay"
                }
            },
            "required": [
                "primer"
            ]
        },
        "general_options": {
            "title": "General options",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-cog",
            "properties": {
                "account": {
                    "type": "string",
                    "default": "None",
                    "description": "Slurm account name (required for -profile slurm)"
                },
                "help": {
                    "type": "boolean",
                    "description": "Print pipeline help message"
                },
                "version": {
                    "type": "boolean",
                    "description": "Print pipeline version"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/pcr_parameters"
        },
        {
            "$ref": "#/definitions/general_options"
        }
    ]
}