cidc_schemas/schemas/templates/assays/tcr_adaptive_template.json
{
"title": "TCRseq [Adaptive] assay template",
"description": "TCR expression data submission via Adaptive's TSV 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",
"allow_empty": true
},
"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",
"allow_empty": true
}
},
"prism_data_object_pointer": "/records/-",
"data_columns": {
"Samples": {
"cimac id": {
"merge_pointer": "0/cimac_id",
"type_ref": "sample.json#properties/cimac_id"
},
"tsv reads": {
"merge_pointer": "0/tsv_file",
"gcs_uri_format": "{protocol identifier}/tcr/{batch id}/{cimac id}/reads.tsv",
"is_artifact": "1",
"type_ref": "assays/components/local_file.json#properties/file_path"
}
}
}
},
"Controls": {
"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"
},
"batch id": {
"merge_pointer": "0/batch_id",
"type_ref": "assays/tcr_assay.json#properties/batch_id"
}
},
"prism_data_object_pointer": "0/controls/-",
"data_columns": {
"Controls": {
"control id": {
"merge_pointer": "0/id",
"type_ref": "assays/tcr_assay.json#definitions/control/properties/id"
},
"tsv reads": {
"merge_pointer": "0/tsv_file",
"gcs_uri_format": "{protocol identifier}/tcr/{batch id}/controls/{control id}/reads.tsv",
"is_artifact": "1",
"type_ref": "assays/components/local_file.json#properties/file_path"
}
}
}
}
}
}
}