CIMAC-CIDC/cidc-schemas

{
  "title": "RNA expression [FASTQ] assay template",
  "description": "RNA expression data submission via FASTQ files.",
  "properties": {
    "worksheets": {
      "RNA": {
        "prism_preamble_object_schema" : "assays/rna_assay-v0.json",
        "prism_preamble_object_pointer" : "/assays/rna/-",
        "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"
          },
          "enrichment method": {
            "merge_pointer": "0/enrichment_method",
            "type_ref": "assays/rna_assay-v0.json#properties/enrichment_method"
          },
          "enrichment kit": {
            "merge_pointer": "0/enrichment_vendor_kit",
            "type_ref": "assays/rna_assay-v0.json#properties/enrichment_vendor_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"
          }
        },
        "data_columns": {
          "Samples": {
            "cimac id": {
              "merge_pointer": "0/cimac_id",
              "type_ref": "sample.json#properties/cimac_id"
            },
            "forward fastq": {
              "merge_pointer": "0/files/r1",
              "gcs_uri_format": "{protocol identifier}/rna/{cimac id}/r1_{num}.fastq.gz",
              "is_artifact": "multi",
              "type_ref": "assays/components/multiple_local_files.json#properties/file_path_list"
            },
            "reverse fastq": {
              "merge_pointer": "0/files/r2",
              "gcs_uri_format": "{protocol identifier}/rna/{cimac id}/r2_{num}.fastq.gz",
              "is_artifact" : "multi",
              "type_ref": "assays/components/multiple_local_files.json#properties/file_path_list"
            },
            "library yield ng": {
              "merge_pointer": "0/library_yield_ng",
              "type_ref": "assays/rna_assay-v0.json#properties/records/items/properties/library_yield_ng"
            },
            "dv200": {
              "merge_pointer": "0/dv200",
              "type_ref": "assays/rna_assay-v0.json#properties/records/items/properties/dv200"
            },
            "rqs": {
              "merge_pointer": "0/rqs",
              "type_ref": "assays/rna_assay-v0.json#properties/records/items/properties/rqs"
            },
            "rin": {
              "merge_pointer": "0/rin",
              "type_ref": "assays/rna_assay-v0.json#properties/records/items/properties/rin",
              "allow_empty": true
            },
            "quality flag": {
              "merge_pointer": "0/quality_flag",
              "type_ref": "assays/rna_assay-v0.json#properties/records/items/properties/quality_flag",
              "type": "number"
            }
          }
        }
      }
    }
  }
}