CIMAC-CIDC/cidc-schemas

{
  "title": "TCRseq [FASTQ] assay template",
  "description": "TCR expression data submission via FASTQ files.",
  "properties": {
    "worksheets": {
      "TCR": {
        "prism_preamble_object_schema" : "assays/tcr_assay.json",
        "prism_preamble_object_pointer" : "/assays/tcr/0",
        "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"
          },
          "sequencer platform": {
            "merge_pointer": "0/sequencer_platform",
            "type_ref": "assays/components/ngs_assay_core.json#properties/sequencer_platform"
          },
          "batch id": {
            "merge_pointer": "0/batch_id",
            "type_ref": "assays/tcr_assay.json#properties/batch_id"
          },
          "sequencing run date": {
            "merge_pointer": "0/sequencing_run_date",
            "type_ref": "assays/tcr_assay.json#properties/sequencing_run_date"
          },
          "sample sheet": {
            "merge_pointer": "0/sample_sheet",
            "gcs_uri_format": "{protocol identifier}/tcr/{batch id}/SampleSheet.csv",
            "is_artifact": 1,
            "type_ref": "assays/components/local_file.json#properties/file_path"
          }
        },
        "prism_data_object_pointer": "/records/0/files/replicates/-",
        "data_columns": {
          "Replicates": {
            "cimac id": {
              "merge_pointer": "3/cimac_id",
              "type_ref": "sample.json#properties/cimac_id"
            },
            "replicate id": {
              "merge_pointer": "/replicate_id",
              "type_ref": "assays/tcr_assay.json#definitions/replicate/properties/replicate_id"
            },
            "read 1": {
              "merge_pointer": "0/r1/-",
              "gcs_uri_format": "{protocol identifier}/tcr/{batch id}/{cimac id}/replicate_{replicate id}/r1.fastq.gz",
              "is_artifact": "1",
              "type_ref": "assays/components/local_file.json#properties/file_path"
            },
            "read 2": {
              "merge_pointer": "0/r2/-",
              "gcs_uri_format": "{protocol identifier}/tcr/{batch id}/{cimac id}/replicate_{replicate id}/r2.fastq.gz",
              "is_artifact" : "1",
              "type_ref": "assays/components/local_file.json#properties/file_path"
            },
            "index 1": {
              "merge_pointer": "0/i1/-",
              "gcs_uri_format": "{protocol identifier}/tcr/{batch id}/{cimac id}/replicate_{replicate id}/i1.fastq.gz",
              "is_artifact": "1",
              "type_ref": "assays/components/local_file.json#properties/file_path"
            },
            "index 2": {
              "merge_pointer": "0/i2/-",
              "gcs_uri_format": "{protocol identifier}/tcr/{batch id}/{cimac id}/replicate_{replicate id}/i2.fastq.gz",
              "is_artifact" : "1",
              "type_ref": "assays/components/local_file.json#properties/file_path"
            },
            "rna quantity": {
              "merge_pointer": "0/rna_quantity_ng",
              "type_ref": "assays/tcr_assay.json#definitions/replicate/properties/rna_quantity_ng"
            }
          }
        }
      }
    }
  }
}