nextflow_schema.template.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "",
    "title": "MAGMA pipeline parameters",
    "description": "",
    "type": "object",
    "definitions": {
        "input_output_options": {
            "title": "Input/Output options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "samplesheet": {
                    "type": "string",
                    "fa_icon": "fas fa-table",
                    "default": "${projectDir}/resources/2samples.txt",
                    "description": "The location of input samplesheet, by default it uses 2 samples."
                },
                "outdir": {
                    "type": "string",
                    "fa_icon": "fas fa-folder-open",
                    "default": "${projectDir}/results",
                    "description": "The output directory for the results of the analysis."
                }
            },
            "required": [
                "samplesheet",
                "outdir"
            ],
            "fa_icon": "fas fa-terminal"
        },
        "reference_files_options": {
            "title": "Reference files options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "fasta": {
                    "type": "string",
                    "fa_icon": "fas fa-file-code",
                    "default": "s3://nf-tower-data/gatk4-germline-snps-indels-nf/references/Homo_sapiens_assembly38.fasta",
                    "default": "${projectDir}/resources/Homo_sapiens_assembly38.fasta",
                    "description": "The location of input reference fasta file."
                }
            },
            "required": [
                "fasta"
            ],
            "fa_icon": "fas fa-anchor",
            "help_text": ""
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/reference_files_options"
        }
    ]
}