config.schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "id": "config.schema.json",
    "name": "Schema for HLA-KIR Imputation Workflow",
    "type": "object",
    "required": ["project"],
    "properties": {
        "KIRIMP_PANEL_URL": {
            "type": "string",
            "default": "http://imp.science.unimelb.edu.au/kir/static/kirimp.uk1.snp.info.csv"
        },
        "SHAPEIT_GENMAP_URL": {
            "type": "string",
            "default": "https://github.com/odelaneau/shapeit4/blob/master/maps/genetic_maps.b37.tar.gz?raw=true"
        },
        "BCFTOOLS_THREADS": {
            "type": "integer",
            "default": 4
        },
        "PLINK_THREADS": {
            "type": "integer",
            "default": 4
        },
        "SHAPEIT_THREADS": {
            "type": "integer",
            "default": 4
        },
        "FREQ_ENCODE_SNPS_THREADS": {
            "type": "integer",
            "default": 4
        },
        "project": {
            "$ref": "#/definitions/project",
            "description": "settings for a specific run"
        }
    },
    "definitions": {
        "project": {
            "type": "object",
            "patternProperties": {
                "^[^./]+$": {
                    "type": "object",
                    "id": "project_id",
                    "additionalProperties": false,
                    "properties": {
                        "liftover": {
                            "$ref": "#/definitions/liftover",
                            "description": "settings relating to converting refernce hg16/hg17/hg18 --> hg19",
                            "default": {
                                "reference": "HG18"
                            }
                        },
                        "freq_encode_snps": {
                            "$ref": "#/definitions/freq_encode_snps",
                            "description": "setting for re-encoding vcf variants to reference panel frequency",
                            "default": {
                                "vcf": "output/{project}/liftover/04_hg19_vcf/{project}.{reference}ToHg19.vcf.gz",
                                "additional": "--outlier-threshold 0.1"
                            }
                        },
                        "shapeit": {
                            "$ref": "#/definitions/shapeit",
                            "description": "setting for shapeit phasing of variants",
                            "default": {
                                "vcf": "output/{project}/kirimp/01_freq_encode_snps/{project}.vcf.gz",
                                "gmap": "input/meta/shapeit/kirimp.chr19.gmap.txt.gz",
                                "pbwt": 8,
                                "pbwt-modulo": 8,
                                "regions": [19],
                                "states": 500,
                                "min_missing": 0.25,
                                "v2_additional": "",
                                "v4_additional": ""
                            }
                        }
                    }
                }
            },
            "additionalProperties": false
        },
        "liftover": {
            "type": "object",
            "properties": {
                "reference": {
                    "type": "string",
                    "enum": [
                        "HG38",
                        "HG18",
                        "HG17",
                        "HG16",
                        "hg38",
                        "hg18",
                        "hg17",
                        "hg16"
                    ],
                    "default": "hg18"
                },
                "plink": {
                    "type": "string",
                    "pattern": ".+(bed|fam|bim)$",
                    "description": "path to plink bed file (must contain bim/fam in the same directory)"
                },
                "vcf": {
                    "$ref": "#/definitions/vcf"
                }
            }
        },
        "freq_encode_snps": {
            "type": "object",
            "properties": {
                "vcf": {
                    "$ref": "#/definitions/vcf"
                },
                "additional": {
                    "$ref": "#/definitions/additional_params"
                }
            }
        },
        "shapeit": {
            "type": "object",
            "properties": {
                "vcf": {
                    "$ref": "#/definitions/vcf"
                },
                "genmap": {
                    "type": "string",
                    "description": "genetic map to be used with phasing"
                },
                "pbwt": {
                    "type": "integer",
                    "description": "numbers of confitioning neighbours (variant density)"
                },
                "pbwt-modulo": {
                    "type": "integer",
                    "description": "numbers of confitioning neighbours (variant density)"
                },
                "regions": {
                    "type": "array",
                    "items": [{ "type": "number" }],
                    "description": "numbers of confitioning neighbours (variant density)"
                },
                "states": {
                    "type": "integer"
                },
                "min_missing": {
                    "type": "number",
                    "description": "Variants with genotype missing rate higher than this will be discarder"
                },
                "additional": {
                    "$ref": "#/definitions/additional_params"
                }
            }
        },
        "vcf": {
            "type": "string",
            "pattern": ".+(vcf|bcf|vcf.gz)"
        },
        "additional_params": {
            "type": "string",
            "description": "Additional parameters to pass to rules",
            "default": ""
        }
    }
}