nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/UPHL-BioNGS/Donut_Falls/main/nextflow_schema.json",
    "title": "Donut Falls Parameters",
    "description": "Donut Falls is a workflow for assembly from nanopore or nanopore/illumina reads",
    "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": [
                "sample_sheet",
                "outdir"
            ],
            "properties": {
                "sample_sheet": {
                    "type": "string",
                    "description": "csv file with sample,nanopore fastq file,illumina R1 (optional),illuimina R2 (optional)"
                },
                "outdir": { 
                    "type": "string", 
                    "description": "Specifies where results are saved",
                    "default": "donut_falls"
                },
                "sequencing_summary": { 
                    "type": "string", 
                    "description": "input channel for nanopore sequencing summary file (optional)"
                }
            }
        },
        "pipeline_configuration_options": {
            "title": "Pipeline Configuration options",
            "type": "object",
            "description": "Options to configure how the workflow runs.",
            "properties": {
                "assembler": { 
                    "type": "string", 
                    "description": "Specifies which assembler is/assemblers are going to be used.",
                    "default" : "flye"
                }
            }
        },
        "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 customize 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": {
                "config_file": {
                    "type": "boolean",
                    "description" : "Specifies if a config file is copied for the end user. Ends script.",
                    "hidden" : true,
                    "default" : false
                },
                "test":{
                    "type": "boolean",
                    "description": "Downloads test file",
                    "default": false,
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/pipeline_configuration_options"
        },
        {
            "$ref": "#/definitions/generic_options"
        }
    ]
}