{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/atacseq/master/assets/schema_input.json",
    "title": "nf-core/atacseq pipeline - params.input schema",
    "description": "Schema for the file provided with params.input",
    "type": "array",
    "items": {
        "type": "object",
        "properties": {
            "sample": {
                "type": "string",
                "pattern": "^\\S+$",
                "errorMessage": "Sample name must be provided and cannot contain spaces"
            },
            "fastq_1": {
                "type": "string",
                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
            },
            "fastq_2": {
                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
                "anyOf": [
                    {
                        "type": "string",
                        "pattern": "^\\S+\\.f(ast)?q\\.gz$"
                    },
                    {
                        "type": "string",
                        "maxLength": 0
                    }
                ]
            },
            "replicate": {
                "type": "integer",
                "pattern": "^[1-9][0-9]*$",
                "errorMessage": "Integer representing replicate number. Must start from 1..<number of replicates>."
            }
        },
        "required": ["sample", "fastq_1", "replicate"]
    }
}
