{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/local/bactopia/gather_samples/params.json",
    "description": "A flexible pipeline for complete analysis of bacterial genomes",
    "type": "object",
    "definitions": {
        "gather_samples_parameters": {
            "title": "Gather Samples Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "enable_fastq_check": {
                    "type": "boolean",
                    "description": "Run minimum requirement checks for input FASTQs",
                    "help": "This parameter is useful if you are confident your sequences will pass the minimum requirements.",
                    "fa_icon": "fas fa-fast-forward"
                },
                "coverage": {
                    "type": "integer",
                    "default": 0,
                    "description": "Reduce samples to a given coverage",
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "genome_size": {
                    "type": "string",
                    "default": "1",
                    "description": "Expected genome size (bp) for all samples",
                    "help": "If `--species` is used, `min`, `median`, `mean`, or `max` can be used for `--genome_size`",
                    "fa_icon": "fas fa-arrows-alt-h",
                    "hidden": true
                },
                "min_basepairs": {
                    "type": "integer",
                    "description": "The minimum amount of basepairs required to continue downstream analyses.",
                    "default": 2241820,
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "min_reads": {
                    "type": "integer",
                    "description": "The minimum amount of reads required to continue downstream analyses.",
                    "default": 7472,
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "min_coverage": {
                    "type": "integer",
                    "description": "The minimum amount of coverage required to continue downstream analyses.",
                    "default": 10,
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "min_proportion": {
                    "type": "number",
                    "description": "The minimum proportion of basepairs for paired-end reads to continue downstream analyses.",
                    "help": "Example: If set to 0.75 the R1 and R2 must have > 75% proportion of reads (e.g. R1 100bp, R2 75bp, not R1 100bp, R2 50bp)",
                    "default": 0.5,
                    "fa_icon": "fas fa-balance-scale-left",
                    "hidden": true
                },
                "min_genome_size": {
                    "type": "integer",
                    "description": "The minimum estimated genome size allowed for the input sequence to continue downstream analyses.",
                    "default": 100000,
                    "fa_icon": "fas fa-angle-double-down",
                    "hidden": true
                },
                "max_genome_size": {
                    "type": "integer",
                    "description": "The maximum estimated genome size allowed for the input sequence to continue downstream analyses.",
                    "default": 18040666,
                    "fa_icon": "fas fa-angle-double-up",
                    "hidden": true
                },
                "attempts": {
                    "type": "integer",
                    "description": "Maximum times to attempt downloads",
                    "default": 3,
                    "fa_icon": "fas fa-redo",
                    "hidden": true
                },
                "use_ena": {
                    "type": "boolean",
                    "description": "Download FASTQs from ENA",
                    "fa_icon": "fas fa-globe-europe",
                    "hidden": true
                },
                "no_cache": {
                    "type": "boolean",
                    "description": "Skip caching the assembly summary file from ncbi-genome-download",
                    "fa_icon": "fas fa-save",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/gather_samples_parameters"
        }
    ]
}
