schema.json

{
    "$schema": "http://json-schema.org/draft-04/schema#",
    "description": "JSON schema for samples config for the hutspot pipeline",
    "type": "object",
    "additionalProperties": false,
    "required": [
        "samples",
        "reference",
        "dbsnp",
        "known_sites"
    ],
    "optional": [
        "scatter_size",
        "female_threshold",
        "bedfile",
        "coverage_threshold",
        "restrict_BQSR",
        "gatk_jar",
        "multisample_vcf",
        "baitsfile"
    ],
    "properties": {
        "samples": {
            "type": "object",
            "additionalProperties": {
                "description": "sample object",
                "type": "object",
                "required": ["read_groups"],
                "properties": {
                    "read_groups": {
                        "type": "object",
                        "additionalProperties": {
                            "description": "library",
                            "type": "object",
                            "required": ["R1", "R2"],
                            "properties": {
                                "R1": {"type": "string"},
                                "R2": {"type": "string"}
                            }
                        }
                    }
                }
            }
        },
    "reference": {
        "description": "Reference fasta file to map against",
        "type": "string"
    },
    "dbsnp": {
        "description": "VCF file to be used to annotate variants",
        "type": "string"
    },
    "known_sites": {
        "description": "VCF files of known sites, to be used to recalibrate the quality scores",
        "type": "array",
        "minItems": 1
    },
    "scatter_size": {
        "description": "Size of the chunks to split the variant calling into",
        "type": "integer"
    },
    "female_threshold": {
        "description": "Fraction of reads between X and the autosomes to call as female",
        "type": "number"
    },
    "targetsfile": {
        "description": "Bed file of the targets of the capture kit. Used to calculate coverage",
        "type": "string"
    },
    "baitsfile": {
        "description": "Bed file of the baits of the capture kit. Used to calculate picard HsMetrics",
        "type": "string"
    },
    "coverage_threshold": {
        "description": "One or more thresholds to calculate coverage for, one bedfile per value per sample",
        "type": "array",
        "minItems": 1
    },
    "restrict_BQSR": {
        "description": "Restrict BQSR to the listed chromosome",
        "type": "string"
    },
    "multisample_vcf": {
        "description": "Create a true multisample VCF file, in addition to the regular per-sample VCF files",
        "type": "boolean"
    },
    "refflat": {
        "description": "RefFlat file with transcripts",
        "type": "string"
    }
  }
}