{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/bacass/master/assets/schema_input.json",
    "title": "nf-core/bacass pipeline - params.input schema",
    "description": "Schema for the file provided with params.input",
    "type": "array",
    "items": {
        "type": "object",
        "properties": {
            "ID": {
                "type": "string",
                "pattern": "^\\S+$",
                "unique": true,
                "errorMessage": "Sample name must be provided and cannot contain spaces",
                "meta": ["id"]
            },
            "R1": {
                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
                "anyOf": [
                    {
                        "type": ["string", "null"],
                        "exists": true,
                        "pattern": "^(\\S+\\.f(ast)?q\\.gz|NA)$"
                    },
                    {
                        "type": "string",
                        "maxLength": 0
                    }
                ]
            },
            "R2": {
                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
                "anyOf": [
                    {
                        "type": ["string", "null"],
                        "exists": true,
                        "pattern": "^(\\S+\\.f(ast)?q\\.gz|NA)$"
                    },
                    {
                        "type": "string",
                        "maxLength": 0
                    }
                ]
            },
            "LongFastQ": {
                "errorMessage": "FastQ file for long reads cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
                "anyOf": [
                    {
                        "type": ["string", "null"],
                        "exists": true,
                        "pattern": "^(\\S+\\.f(ast)?q\\.gz|NA)$"
                    },
                    {
                        "type": "string",
                        "maxLength": 0
                    }
                ]
            },
            "Fast5": {
                "errorMessage": "A valid path to Fast5 files. Example: ./data/FAST5",
                "anyOf": [
                    {
                        "type": ["string", "null"],
                        "format": "directory-path",
                        "exists": true,
                        "pattern": "^(\\/[\\S\\s]*|NA)$"
                    },
                    {
                        "type": "string",
                        "maxLength": 0
                    }
                ]
            },
            "GenomeSize": {
                "errorMessage": "A number (including decimals) ending with 'm', representing genome size. No spaces allowed.",
                "meta": ["gsize"],
                "anyOf": [
                    {
                        "type": ["string", "null"],
                        "pattern": "(\\b\\d+\\.\\d+m\\b|NA)"
                    },
                    {
                        "type": "string",
                        "maxLength": 0
                    }
                ]
            }
        },
        "required": ["ID"]
    }
}
