{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/conf/schema/clean-yer-reads.json",
    "title": "Clean-Yer-Reads pipeline parameters",
    "description": "Use Bactopia's read QC steps to Clean-Yer-Reads",
    "type": "object",
    "definitions": {
        "input_parameters": {
            "title": "Required Parameters",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "help_text": "",
            "properties": {
                "samples": {
                    "type": "string",
                    "description": "A FOFN (via bactopia prepare) with sample names and paths to FASTQ/FASTAs to process\n",
                    "help": "Created using `bactopia prepare`. Cannot be used with `--R1|--R2` or `--SE`",
                    "fa_icon": "fas fa-file-alt",
                    "header": "### For Procesessing Multiple Samples"
                },
                "R1": {
                    "type": "string",
                    "description": "First set of compressed (gzip) paired-end FASTQ reads (requires --R2 and --sample)",
                    "help": "Requires `--R2` and `--sample`. Cannot be used with `--samples` or `--SE` (unless `--hybrid` used).",
                    "fa_icon": "fas fa-file-archive",
                    "header": "### For Processing A Single Sample"
                },
                "R2": {
                    "type": "string",
                    "description": "Second set of compressed (gzip) paired-end FASTQ reads (requires --R1 and --sample)",
                    "help": "Requires `--R1` and `--sample`. Cannot be used with `--samples` or `--SE` (unless `--hybrid` used).",
                    "fa_icon": "fas fa-file-archive"
                },
                "SE": {
                    "type": "string",
                    "description": "Compressed (gzip) single-end FASTQ reads  (requires --sample)",
                    "help": "Requires `--sample`. Cannot be used with `--samples` or `--R1|--R2` (unless `--hybrid` used).",
                    "fa_icon": "fas fa-file-archive"
                },
                "ont": {
                    "type": "boolean",
                    "default": false,
                    "description": "Treat `--SE` or `--accession` as long reads for analysis. (requires --sample if using --SE)",
                    "fa_icon": "fas fa-level-up"
                },
                "sample": {
                    "type": "string",
                    "description": "Sample name to use for the input sequences\n",
                    "help": "Required when using `--R1|--R2` or `--SE`",
                    "fa_icon": "fas fa-file"
                },
                "accessions": {
                    "type": "string",
                    "description": "A file containing ENA/SRA Experiment accessions or NCBI Assembly accessions to processed",
                    "fa_icon": "fas fa-file-alt",
                    "header": "### For Downloading from SRA/ENA or NCBI Assembly\n  **Note: Downloaded assemblies will have error free Illumina reads simulated for processing.**"
                },
                "accession": {
                    "type": "string",
                    "description": "Sample name to use for the input sequences\n",
                    "help": "Required when using `--R1|--R2` or `--SE`",
                    "fa_icon": "fas fa-font"
                },
                "check_samples": {
                    "type": "boolean",
                    "default": false,
                    "description": "Validate the input FOFN provided by --samples",
                    "fa_icon": "fas fa-level-up"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_parameters"
        }
    ]
}
