CIMAC-CIDC/cidc-schemas

{
  "title": "WES [BAM] assay template",
  "description": "Whole Exome Sequencing (WES) data submission via BAM files.",
  "properties": {
    "worksheets": {
      "WES": {
        "prism_preamble_object_schema" : "assays/wes_assay.json",
        "prism_preamble_object_pointer" : "/assays/wes/-",
        "prism_data_object_pointer" : "/records/-",
        "preamble_rows": {
          "protocol identifier": {
            "merge_pointer": "3/protocol_identifier",
            "type_ref": "clinical_trial.json#properties/protocol_identifier"
          },
          "assay creator": {
            "merge_pointer": "0/assay_creator",
            "type_ref": "assays/components/assay_core.json#properties/assay_creator"
          },
          "sequencing protocol": {
            "merge_pointer": "0/sequencing_protocol",
            "type_ref": "assays/wes_assay.json#properties/sequencing_protocol"
          },
          "library kit": {
            "merge_pointer": "0/library_kit",
            "type_ref": "assays/components/ngs_assay_core.json#properties/library_kit"
          },
          "sequencer platform": {
            "merge_pointer": "0/sequencer_platform",
            "type_ref": "assays/components/ngs_assay_core.json#properties/sequencer_platform"
          },
          "paired end reads": {
            "merge_pointer": "0/paired_end_reads",
            "type_ref": "assays/components/ngs_assay_core.json#properties/paired_end_reads"
          },
          "read length": {
            "merge_pointer": "0/read_length",
            "type_ref": "assays/wes_assay.json#properties/read_length"
          },
          "bait set": {
            "merge_pointer": "0/bait_set",
            "type_ref": "assays/wes_assay.json#properties/bait_set"
          }
        },
        "data_columns": {
          "Samples": {
            "cimac id": {
              "merge_pointer": "0/cimac_id", 
              "type_ref": "sample.json#properties/cimac_id"
            },
            "BAM file": {
              "merge_pointer": "0/files/bam",
              "gcs_uri_format": "{protocol identifier}/wes/{cimac id}/reads_{num}.bam",
              "is_artifact": "multi",
              "type_ref": "assays/components/multiple_local_files.json#properties/file_path_list"            
            },
            "sequencing date": {
              "merge_pointer": "0/sequencing_date",
              "type_ref": "assays/wes_assay.json#definitions/entry/properties/sequencing_date"
            },
            "quality flag": {
              "merge_pointer": "0/quality_flag",
              "type_ref": "assays/wes_assay.json#definitions/entry/properties/quality_flag"
            }
          }
        }
      }
    }
  }
}