docs/old_uploads/wes_analysis_old_template.json
{
"title": "WES analysis template",
"description": "Metadata information for WES Analysis output.",
"prism_template_root_object_schema": "assays/wes_analysis.json",
"prism_template_root_object_pointer": "/analysis/wes_analysis",
"properties": {
"worksheets": {
"WES Analysis": {
"preamble_rows": {
"protocol identifier": {
"merge_pointer": "2/protocol_identifier",
"type_ref": "clinical_trial.json#properties/protocol_identifier"
},
"folder": {
"do_not_merge": true,
"type": "string",
"allow_empty": true
}
},
"prism_data_object_pointer": "/pair_runs/-",
"data_columns": {
"WES Runs": {
"run id": {
"merge_pointer": "/run_id",
"type_ref": "assays/wes_analysis.json#definitions/pair_analysis/properties/run_id",
"process_as": [
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/{run}_error.yaml'",
"merge_pointer": "/error",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/error.yaml",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1,
"allow_empty": true
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/somatic/{run}/{run}_tnscope.output.vcf.gz'",
"merge_pointer": "/somatic/vcf_gz_tnscope_output",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/vcf_gz_tnscope_output.vcf.gz",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/somatic/{run}/{run}_tnscope.filter.vcf.gz'",
"merge_pointer": "/somatic/vcf_gz_tnscope_filter",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/vcf_gz_tnscope_filter.vcf.gz",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/somatic/{run}/{run}_tnscope.filter.maf'",
"merge_pointer": "/somatic/maf_tnscope_filter",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/maf_tnscope_filter.maf",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/somatic/{run}/{run}_tnscope.output.twist.vcf'",
"merge_pointer": "/somatic/tnscope_output_twist_vcf",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/tnscope_output_twist.vcf",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/somatic/{run}/{run}_tnscope.output.twist.maf'",
"merge_pointer": "/somatic/tnscope_output_twist_maf",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/tnscope_output_twist.maf",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/somatic/{run}/{run}_tnscope.output.twist.filtered.vcf'",
"merge_pointer": "/somatic/tnscope_output_twist_filtered_vcf",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/tnscope_output_twist_filtered.vcf",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/somatic/{run}/{run}_tnscope.output.twist.filtered.maf'",
"merge_pointer": "/somatic/tnscope_output_twist_filtered_maf",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/tnscope_output_twist_filtered.maf",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/germline/{run}/{run}_vcfcompare.txt'",
"merge_pointer": "/germline/vcf_compare",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/vcf_compare.txt",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/report/somatic_variants/05_tumor_germline_overlap.tsv'",
"merge_pointer": "/report/tumor_germline_overlap",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/tumor_germline_overlap.tsv",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/report/neoantigens/01_HLA_Results.tsv'",
"merge_pointer": "/neoantigen/HLA_results",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/HLA_results.tsv",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/neoantigen/{run}/combined/{run}.filtered.tsv'",
"merge_pointer": "/neoantigen/combined_filtered",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/combined_filtered.tsv",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/purity/{run}/{run}.optimalpurityvalue.txt'",
"merge_pointer": "/purity/optimal_purity_value",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/optimal_purity_value.txt",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/clonality/{run}/{run}_pyclone.tsv'",
"merge_pointer": "/clonality/clonality_pyclone",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/clonality_pyclone.tsv",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/clonality/{run}/{run}_table.tsv'",
"merge_pointer": "/clonality/clonality_table",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/clonality_table.tsv",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/copynumber/{run}/{run}_cnvcalls.txt'",
"merge_pointer": "/copynumber/copynumber_cnv_calls",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/copynumber_cnvcalls.txt",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/copynumber/{run}/{run}_cnvcalls.txt.tn.tsv'",
"merge_pointer": "/copynumber/copynumber_cnv_calls_tsv",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/copynumber_cnvcalls.txt.tn.tsv",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/msisensor2/{run}/{run}_msisensor.txt'",
"merge_pointer": "/msisensor/msisensor",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/msisensor.txt",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/rna/{run}/{run}.haplotyper.rna.vcf.gz'",
"merge_pointer": "/rna/haplotyper",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/haplotyper.vcf.gz",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1,
"allow_empty": true
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/rna/{run}/{run}_tnscope.filter.neoantigen.vep.rna.vcf'",
"merge_pointer": "/rna/vcf_tnscope_filter_neoantigen",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/vcf_tnscope_filter_neoantigen.vcf",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1,
"allow_empty": true
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/report.tar.gz'",
"merge_pointer": "/report/report",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/report.tar.gz",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/report/WES_Meta/02_WES_Run_Version.tsv'",
"merge_pointer": "/report/wes_run_version",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/wes_run_version.tsv",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/report/config.yaml'",
"merge_pointer": "/report/config",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/config.yaml",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/report/metasheet.csv'",
"merge_pointer": "/report/metasheet",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/metasheet.csv",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/report/json/{run}.wes.json'",
"merge_pointer": "/report/wes_sample_json",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/wes_sample.json",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
}
]
},
"normal cimac id": {
"merge_pointer": "/normal/cimac_id",
"type_ref": "sample.json#properties/cimac_id",
"process_as": [
{
"parse_through": "lambda id: f'{folder or \"\"}analysis/align/{id}/{id}.sorted.dedup.bam'",
"merge_pointer": "/normal/alignment/align_sorted_dedup",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/sorted.dedup.bam",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda id: f'{folder or \"\"}analysis/align/{id}/{id}.sorted.dedup.bam.bai'",
"merge_pointer": "/normal/alignment/align_sorted_dedup_index",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/sorted.dedup.bam.bai",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda id: f'{folder or \"\"}analysis/optitype/{id}/{id}_result.tsv'",
"merge_pointer": "/normal/optitype/optitype_result",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/optitype_result.tsv",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda id: f'{folder or \"\"}analysis/xhla/{id}/report-{id}-hla.json'",
"merge_pointer": "/normal/optitype/xhla_report_hla",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/xhla_report_hla.json",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda id: f'{folder or \"\"}analysis/metrics/{id}/{id}_coverage_metrics.txt'",
"merge_pointer": "/normal/metrics/coverage_metrics",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/coverage_metrics.txt",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda id: f'{folder or \"\"}analysis/metrics/{id}/{id}_target_metrics.txt'",
"merge_pointer": "/normal/metrics/target_metrics",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/target_metrics.txt",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda id: f'{folder or \"\"}analysis/metrics/{id}/{id}_coverage_metrics.sample_summary.txt'",
"merge_pointer": "/normal/metrics/coverage_metrics_summary",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/coverage_metrics_summary.txt",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda id: f'{folder or \"\"}analysis/germline/{id}/{id}_haplotyper.targets.vcf.gz'",
"merge_pointer": "/normal/germline/haplotyper_targets",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/normal/{normal cimac id}/haplotyper_targets.vcf.gz",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
}
]
},
"tumor cimac id": {
"merge_pointer": "/tumor/cimac_id",
"type_ref": "sample.json#properties/cimac_id",
"process_as": [
{
"parse_through": "lambda id: f'{folder or \"\"}analysis/align/{id}/{id}.sorted.dedup.bam'",
"merge_pointer": "/tumor/alignment/align_sorted_dedup",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/tumor/{tumor cimac id}/sorted.dedup.bam",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda id: f'{folder or \"\"}analysis/align/{id}/{id}.sorted.dedup.bam.bai'",
"merge_pointer": "/tumor/alignment/align_sorted_dedup_index",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/tumor/{tumor cimac id}/sorted.dedup.bam.bai",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda id: f'{folder or \"\"}analysis/optitype/{id}/{id}_result.tsv'",
"merge_pointer": "/tumor/optitype/optitype_result",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/tumor/{tumor cimac id}/optitype_result.tsv",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda id: f'{folder or \"\"}analysis/xhla/{id}/report-{id}-hla.json'",
"merge_pointer": "/tumor/optitype/xhla_report_hla",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/tumor/{tumor cimac id}/xhla_report_hla.json",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda id: f'{folder or \"\"}analysis/metrics/{id}/{id}_coverage_metrics.txt'",
"merge_pointer": "/tumor/metrics/coverage_metrics",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/tumor/{tumor cimac id}/coverage_metrics.txt",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda id: f'{folder or \"\"}analysis/metrics/{id}/{id}_target_metrics.txt'",
"merge_pointer": "/tumor/metrics/target_metrics",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/tumor/{tumor cimac id}/target_metrics.txt",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda id: f'{folder or \"\"}analysis/metrics/{id}/{id}_coverage_metrics.sample_summary.txt'",
"merge_pointer": "/tumor/metrics/coverage_metrics_summary",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/tumor/{tumor cimac id}/coverage_metrics_summary.txt",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
},
{
"parse_through": "lambda id: f'{folder or \"\"}analysis/germline/{id}/{id}_haplotyper.targets.vcf.gz'",
"merge_pointer": "/tumor/germline/haplotyper_targets",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/tumor/{tumor cimac id}/haplotyper_targets.vcf.gz",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
}
]
},
"comments": {
"type_ref": "assays/wes_analysis.json#definitions/pair_analysis/properties/comments",
"merge_pointer": "0/comments",
"allow_empty": true
}
}
}
},
"Excluded Samples": {
"prism_data_object_pointer": "/excluded_samples/-",
"data_columns": {
"Samples Excluded From Analysis": {
"cimac id": {
"type_ref": "sample.json#properties/cimac_id",
"merge_pointer": "0/cimac_id"
},
"reason": {
"type_ref": "assays/components/excluded_samples.json#items/properties/reason_excluded",
"merge_pointer": "0/reason_excluded"
}
}
}
}
}
}
}