nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/jvfe/ukb_ppp_gsmr/master/nextflow_schema.json",
    "title": "jvfe/ukb_ppp_gsmr pipeline parameters",
    "description": "A pipeline for mendelian randomization",
    "type": "object",
    "definitions": {
        "sumstats": {
            "title": "Sumstats",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "exposures": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/csv",
                    "schema": "/assets/schema_exposures.json",
                    "description": "Samplesheet of exposure sumstats"
                },
                "outcomes": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/csv",
                    "schema": "/assets/schema_outcomes.json",
                    "description": "Samplesheet of outcome sumstats"
                }
            }
        },
        "gwas_references": {
            "type": "object",
            "title": "GWAS References",
            "properties": {
                "references": {
                    "type": "string"
                },
                "twosmr_ref": {
                    "type": "string"
                }
            }
        },
        "skip_steps": {
            "title": "Skip steps",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "skip_gsmr": {
                    "type": "boolean",
                    "description": "Skip GSMR"
                },
                "skip_2smr": {
                    "type": "boolean"
                }
            }
        },
        "nf_validation": {
            "title": "nf-validation",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "validationSkipDuplicateCheck": {
                    "type": "boolean",
                    "hidden": true
                },
                "validationS3PathCheck": {
                    "type": "string",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/sumstats"
        },
        {
            "$ref": "#/definitions/gwas_references"
        },
        {
            "$ref": "#/definitions/skip_steps"
        },
        {
            "$ref": "#/definitions/nf_validation"
        }
    ]
}