nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/your-username/your-repo/master/nextflow_schema.json",
    "title": "Your Pipeline Parameters",
    "description": "Schema for the parameters of your Nextflow pipeline",
    "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": ["reads", "output"],
            "properties": {
                "reads": {
                    "type": "string",
                    "format": "path",
                    "description": "Path to input reads",
                    "help_text": "Path to input reads (e.g., fastq files)",
                    "fa_icon": "fas fa-folder-open"
                },
                "output": {
                    "type": "string",
                    "format": "path",
                    "description": "Path to the output directory",
                    "help_text": "The output directory where results will be saved",
                    "fa_icon": "fas fa-folder-open"
                }
            }
        },
        "processing_options": {
            "title": "Processing Options",
            "type": "object",
            "fa_icon": "fas fa-cogs",
            "description": "Parameters to customize the processing behavior.",
            "properties": {
                "sample_size": {
                    "type": "integer",
                    "description": "Number of samples to process",
                    "default": 1000000,
                    "minimum": 100,
                    "fa_icon": "fas fa-sort-numeric-down"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/processing_options"
        }
    ]
}