cidc_schemas/schemas/templates/assays/wes_fastq_template.json
{
"title": "WES [FASTQ] assay template",
"description": "Whole Exome Sequencing (WES) data submission via FASTQ 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",
"allow_empty": true
},
"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"
},
"lane": {
"do_not_merge": true,
"type": "string"
},
"forward fastq": {
"merge_pointer": "0/files/r1/0",
"gcs_uri_format": "{protocol identifier}/wes/{cimac id}/r1_L{lane}.fastq.gz",
"is_artifact": 1,
"type_ref": "assays/components/local_file.json#properties/file_path"
},
"reverse fastq": {
"merge_pointer": "0/files/r2/0",
"gcs_uri_format": "{protocol identifier}/wes/{cimac id}/r2_L{lane}.fastq.gz",
"is_artifact" : 1,
"type_ref": "assays/components/local_file.json#properties/file_path"
},
"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"
}
}
}
}
}
}
}