{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/cutandrun/master/assets/schema_input.json",
    "title": "nf-core/cutandrun pipeline - params.input schema",
    "description": "Schema for the file provided with params.input",
    "type": "array",
    "items": {
        "type": "object",
        "properties": {
            "group": {
                "type": "string",
                "pattern": "^\\S+$",
                "errorMessage": "Sample group must be provided and cannot contain spaces"
            },
            "replicate": {
                "type": "integer",
                "pattern": "^[0-9]*$",
                "errorMessage": "Biological Replicate number within the group - technical replicates must have the same replicate number"
            },
            "control_group": {
                "type": "integer",
                "pattern": "^[0-9]*$",
                "errorMessage": "Group ID that matches to the IgG control group (if provided) - otherwise set to 0"
            },
            "fastq_1": {
                "type": "string",
                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
            },
            "fastq_2": {
                "type": "string",
                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                "errorMessage": "FastQ file for reads 2 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
            }
        },
        "required": [
            "sample",
            "replicate",
            "control_group",
            "fastq_1",
            "fastq_2"
        ]
    }
}
