CIMAC-CIDC/cidc-schemas

{
    "title": "Metadata manifest for WES analysis pairing",
    "description": "Metadata manifest for tumor / normal pairing for WES assay analysis.",
    "properties": {
        "worksheets": {

            "Pairing": {
                "prism_preamble_object_schema": "clinical_trial.json",
                "prism_preamble_object_pointer": "#",
                "preamble_rows": {
                    "protocol identifier": {
                        "merge_pointer": "/protocol_identifier",
                        "type_ref": "clinical_trial.json#properties/protocol_identifier"
                    }
                },
                "prism_data_object_pointer": "/analysis/wes_analysis/pair_runs/-",
                "data_columns": {
                    "Pair": {
                        "tumor sample CIMAC ID": {
                            "merge_pointer": "/tumor/cimac_id",
                            "type_ref": "sample.json#properties/cimac_id",
                            "process_as": [
                                {
                                    "merge_pointer": "/run_id",
                                    "type_ref": "assays/wes_analysis.json#definitions/pair_analysis/properties/run_id"
                                }
                            ] 
                        },
                        "normal sample CIMAC ID": {
                            "merge_pointer": "/normal/cimac_id",
                            "type_ref": "sample.json#properties/cimac_id"
                        }
                    }
                }
            },
            "Tumor-only": {
                "prism_preamble_object_schema": "clinical_trial.json",
                "prism_preamble_object_pointer": "#",
                "preamble_rows": {
                    "protocol identifier": {
                        "merge_pointer": "/protocol_identifier",
                        "type_ref": "clinical_trial.json#properties/protocol_identifier"
                    }
                },
                "prism_data_object_pointer": "/analysis/wes_tumor_only_analysis/runs/-",
                "data_columns": {
                    "Tumor-only": {
                        "tumor sample CIMAC ID": {
                            "merge_pointer": "/tumor/cimac_id",
                            "type_ref": "sample.json#properties/cimac_id",
                            "process_as": [
                                {
                                    "merge_pointer": "/run_id",
                                    "type_ref": "assays/wes_tumor_only_analysis.json#definitions/sample_analysis/properties/run_id"
                                }
                            ] 
                        }
                    }
                }
            }
        }
    }
}