nci-cidc-schemas 0.26.29__tar.gz → 0.26.32__tar.gz

{nci_cidc_schemas-0.26.29/nci_cidc_schemas.egg-info → nci_cidc_schemas-0.26.32}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nci_cidc_schemas
-Version: 0.26.29
+Version: 0.26.32
 Summary: The CIDC data model and tools for working with it.
 Home-page: https://github.com/NCI-CIDC/cidc-schemas
 Author: NCI

{nci_cidc_schemas-0.26.29 → nci_cidc_schemas-0.26.32}/cidc_schemas/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = """NCI"""
 __email__ = "nci-cidc-tools-admin@mail.nih.gov"
-__version__ = "0.26.29"
+__version__ = "0.26.32"

{nci_cidc_schemas-0.26.29 → nci_cidc_schemas-0.26.32}/cidc_schemas/json_validation.py

@@ -110,10 +110,10 @@ class _Validator(jsonschema.Draft7Validator):
                     ref_path_pattern = scope["ref_path_pattern"]
                     # If there are no cached values for this ref path pattern, collect them
                     if ref_path_pattern not in self._in_doc_refs_cache:
-                        self._in_doc_refs_cache[
-                            ref_path_pattern
-                        ] = self._get_values_for_path_pattern(
-                            ref_path_pattern, instance
+                        self._in_doc_refs_cache[ref_path_pattern] = (
+                            self._get_values_for_path_pattern(
+                                ref_path_pattern, instance
+                            )
                         )
 
         # see: https://docs.python.org/3/library/contextlib.html

{nci_cidc_schemas-0.26.29 → nci_cidc_schemas-0.26.32}/cidc_schemas/prism/constants.py

@@ -51,6 +51,7 @@ SUPPORTED_ANALYSES = [
     "tcr_analysis",
     "wes_analysis",
     "wes_tumor_only_analysis",
+    "ctdna_analysis",
 ]
 
 SUPPORTED_TEMPLATES = SUPPORTED_ASSAYS + SUPPORTED_MANIFESTS + SUPPORTED_ANALYSES
@@ -62,6 +63,7 @@ ASSAY_TO_FILEPATH: Dict[str, str] = {
     "rna_level1_analysis": "rna/",
     "wes_analysis": "wes/",
     "wes_tumor_only_analysis": "wes_tumor_only/",
+    "ctdna_analysis": "ctdna/",
     # assay specifics removed
     "atacseq_fastq": "atacseq/",
     "rna_bam": "rna/",

{nci_cidc_schemas-0.26.29 → nci_cidc_schemas-0.26.32}/cidc_schemas/prism/core.py

@@ -1,4 +1,5 @@
 """Build metadata dictionaries from Excel files."""
+
 import logging
 import base64
 import hmac

{nci_cidc_schemas-0.26.29 → nci_cidc_schemas-0.26.32}/cidc_schemas/prism/extra_metadata.py

@@ -1,4 +1,5 @@
 """Parsers for extracting extra metadata from files containing molecular data."""
+
 import logging
 import re
 from codecs import BOM_UTF8

{nci_cidc_schemas-0.26.29 → nci_cidc_schemas-0.26.32}/cidc_schemas/prism/pipelines.py

@@ -1,4 +1,5 @@
 """Analysis pipeline configuration generators."""
+
 from collections import defaultdict
 from datetime import datetime
 from io import BytesIO
@@ -15,6 +16,7 @@ from ..util import load_pipeline_config_template, participant_id_from_cimac
 
 logger = logging.getLogger(__file__)
 
+
 # Note, bucket names must be all lowercase, dash, and underscore
 # https://cloud.google.com/storage/docs/naming-buckets#requirements
 def RNA_GOOGLE_BUCKET_PATH_FN(trial_id: str, batch_num: int) -> str:

{nci_cidc_schemas-0.26.29 → nci_cidc_schemas-0.26.32}/cidc_schemas/schemas/artifacts/artifact_core.json

@@ -89,6 +89,7 @@
         "JSON",
         "YAML",
         "PDF",
+        "RDATA",
         "[NOT SET]"
       ]
     },

nci_cidc_schemas-0.26.32/cidc_schemas/schemas/artifacts/artifact_rdata.json

@@ -0,0 +1,51 @@
+{
+  "$schema": "metaschema/strict_meta_schema.json#",
+  "$id": "rdata_artifact",
+  "title": "RData Artifact",
+  "type": "object",
+  "description": "Information about a rdata file.",
+  "additionalProperties": false,
+  "properties": {
+    "data_format": {
+      "description": "Data format.",
+      "const": "RDATA"
+    },
+    "upload_placeholder": {
+      "$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
+    },
+    "artifact_creator": {
+      "$ref": "artifacts/artifact_core.json#properties/artifact_creator"
+    },
+    "uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
+    "uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
+    "file_name": {
+      "$ref": "artifacts/artifact_core.json#properties/file_name"
+    },
+    "object_url": {
+      "$ref": "artifacts/artifact_core.json#properties/object_url"
+    },
+    "uploaded_timestamp": {
+      "$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
+    },
+    "file_size_bytes": {
+      "$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
+    },
+    "md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
+    "crc32c_hash": {
+      "$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
+    },
+    "visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
+    "artifact_category": {
+      "$ref": "artifacts/artifact_core.json#properties/artifact_category"
+    },
+    "facet_group": {
+      "$ref": "artifacts/artifact_core.json#properties/facet_group"
+    }
+  },
+  "allOf": [
+    {
+      "$ref": "artifacts/artifact_core.json"
+    }
+  ],
+  "mergeStrategy": "objectMerge"
+}

{nci_cidc_schemas-0.26.29 → nci_cidc_schemas-0.26.32}/cidc_schemas/schemas/assays/components/available_ngs_analyses.json

@@ -13,6 +13,9 @@
     "wes_tumor_only_analysis": {
       "$ref": "assays/wes_tumor_only_analysis.json"
     },
+    "ctdna_analysis": {
+      "$ref": "assays/ctdna_analysis.json"
+    },
     "wes_analysis_old": {
       "$ref": "assays/wes_analysis.json"
     },

nci_cidc_schemas-0.26.32/cidc_schemas/schemas/assays/ctdna_analysis.json

@@ -0,0 +1,52 @@
+{
+  "$schema": "metaschema/strict_meta_schema.json#",
+  "$id": "ctdna_analysis",
+  "title": "ctDNA analysis",
+  "type": "object",
+  "description": "Combined analysis files for the ctDNA assay.",
+
+  "definitions": {
+    "sample_analysis": {
+      "type": "object",
+      "description": "ctDNA assay output files for a tumor normal pair of samples.",
+
+      "required": [
+        "run_id",
+        "tumor"
+      ],
+      "additionalProperties": false,
+      "properties": {
+        "run_id": {
+          "type": "string",
+          "description": "An id used as if this was a paired analysis run."
+        },
+        "error": { "$ref": "assays/wes_core.json#properties/error" },
+        "tumor": { "$ref": "assays/wes_assay.json#definitions/sample_analysis" },
+        "comments": {
+          "type": "string",
+          "description": "Comments on the tumor-only analysis run."
+        }
+      }
+    }
+  },
+
+  "required": [],
+  "additionalProperties": false,
+  "properties": {
+    "runs": {
+      "type": "array",
+      "items": {
+        "$ref": "assays/ctdna_analysis.json#definitions/sample_analysis"
+      },
+      "mergeStrategy": "arrayMergeById",
+      "mergeOptions": {
+        "$comment": "TODO fix to merge by a pair of normal and tumor ids. It requires improvements to the merge strategy code.",
+        "idRef": "/run_id"
+      }
+    },
+    "batch_id": {"$ref": "assays/tcr_assay.json#properties/batch_id"},
+    "excluded_samples": {
+      "$ref": "assays/components/excluded_samples.json"
+    }
+  }
+}

{nci_cidc_schemas-0.26.29 → nci_cidc_schemas-0.26.32}/cidc_schemas/schemas/assays/ctdna_assay.json

@@ -41,6 +41,9 @@
 				"bias_qc_plots": {"$ref": "artifacts/artifact_pdf.json"},
 				"optimal_solution": {"$ref": "artifacts/artifact_zip.json"},
 				"other_solutions": {"$ref": "artifacts/artifact_zip.json"},
+				"on_premise_corrected_depth_file": {"$ref": "artifacts/artifact_text.json"},
+				"on_premise_parameters_file": {"$ref": "artifacts/artifact_text.json"},
+				"on_premise_rdata_file": {"$ref": "artifacts/artifact_rdata.json"},
 
 				"fraction_cna_subclonal": {
 					"description": "Fraction of copy number altered bins that are subclonal. Accepts NaN. (0-1)",

{nci_cidc_schemas-0.26.29 → nci_cidc_schemas-0.26.32}/cidc_schemas/schemas/assays/ihc_assay.json

@@ -129,7 +129,8 @@
             "enum": [
                 "Vectra 2.0",
                 "Hamamatsu",
-                "AT2 Turbo"
+                "AT2 Turbo",
+                "Akoya PhenoImager HT"
             ]
         },
         "staining_platform": {
@@ -171,4 +172,4 @@
         "records"
     ],
     "mergeStrategy": "objectMerge"
-}
+}

nci_cidc_schemas-0.26.32/cidc_schemas/schemas/templates/analyses/ctdna_analysis_template.json

@@ -0,0 +1,121 @@
+{
+    "title": "ctDNA analysis template",
+    "description": "ctDNA analysis submission.",
+    "prism_template_root_object_schema": "assays/ctdna_analysis.json",
+    "prism_template_root_object_pointer": "/analysis/ctdna_analysis",
+    "properties": {
+        "worksheets": {
+            "ctDNA 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
+                    },
+                    "batch id": {
+                        "merge_pointer": "0/batch_id",
+                        "type_ref": "assays/tcr_assay.json#properties/batch_id"
+                    }
+                },
+                "prism_data_object_pointer": "/runs/-",
+                "data_columns": {
+                    "ctDNA Runs": {
+                        "run id": {
+                            "merge_pointer": "/run_id",
+                            "type_ref": "assays/ctdna_analysis.json#definitions/sample_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}/ctdna/{run id}/analysis/error.yaml",
+                                    "type_ref": "assays/components/local_file.json#properties/file_path",
+                                    "is_artifact": 1,
+                                    "allow_empty": true
+                                }
+                            ]
+                        },
+                        "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}/ctdna/{run id}/analysis/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}/ctdna/{run id}/analysis/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/align/{id}/{id}_recalibrated.bam'",
+                                    "merge_pointer": "/tumor/alignment/align_recalibrated",
+                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/recalibrated.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}_recalibrated.bam.bai'",
+                                    "merge_pointer": "/tumor/alignment/align_recalibrated_index",
+                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/recalibrated.bam.bai",
+                                    "type_ref": "assays/components/local_file.json#properties/file_path",
+                                    "is_artifact": 1
+                                },
+                                {
+                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/hlahd/{id}/result/{id}_final.result.txt'",
+                                    "merge_pointer": "/tumor/hla/hla_final_result",
+                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/hla_final_result.txt",
+                                    "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/hla/optitype_result",
+                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/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/hla/xhla_report_hla",
+                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/xhla_report_hla.json",
+                                    "type_ref": "assays/components/local_file.json#properties/file_path",
+                                    "is_artifact": 1
+                                }
+                            ]
+                        },
+                        "comments": {
+                            "type_ref": "assays/ctdna_analysis.json#definitions/sample_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"
+                        }
+                    }
+                }
+            }
+        }
+    }
+}

{nci_cidc_schemas-0.26.29 → nci_cidc_schemas-0.26.32}/cidc_schemas/schemas/templates/assays/ctdna_template.json

@@ -93,6 +93,24 @@
                 "merge_pointer": "0/tumor_fraction",
                 "type_ref": "assays/ctdna_assay.json#definitions/entry/properties/tumor_fraction"
             },
+            "on premise corrected depth file": {
+                "merge_pointer": "0/on_premise_corrected_depth_file",
+                "type_ref": "assays/components/local_file.json#properties/file_path",
+                "is_artifact": 1,
+                "gcs_uri_format": "{protocol identifier}/ctdna/{batch id}/{cimac id}/OnPrem.correctedDepth.txt"
+            },
+            "on premise parameters file": {
+                "merge_pointer": "0/on_premise_parameters_file",
+                "type_ref": "assays/components/local_file.json#properties/file_path",
+                "is_artifact": 1,
+                "gcs_uri_format": "{protocol identifier}/ctdna/{batch id}/{cimac id}/OnPrem.params.txt"
+            },
+            "on premise rdata file": {
+                "merge_pointer": "0/on_premise_rdata_file",
+                "type_ref": "assays/components/local_file.json#properties/file_path",
+                "is_artifact": 1,
+                "gcs_uri_format": "{protocol identifier}/ctdna/{batch id}/{cimac id}/OnPrem.RData"
+            },
             "comments": {
                 "type_ref": "assays/ctdna_assay.json#definitions/entry/properties/comments",
                 "merge_pointer": "0/comments",

{nci_cidc_schemas-0.26.29 → nci_cidc_schemas-0.26.32}/cidc_schemas/template.py

@@ -232,6 +232,7 @@ def _initialize_template_schema(name: str, title: str, pointer: str):
         "rna": "RNA sequencing Level 1",
         "wes": "Whole Exome Sequencing (WES) Tumor-Normal Paired",
         "wes_tumor_only": "Whole Exome Sequencing (WES) Tumor-Only",
+        "ctDNA": "ctDNA",
     }[name]
 
     # static
@@ -419,6 +420,7 @@ def _convert_api_to_template(name: str, schema: dict, assay_schema: dict):
         "rna": "RNAseq level 1",
         "wes": "WES",
         "wes_tumor_only": "WES tumor-only",
+        "ctdna": "ctDNA",
     }[name]
 
     pointer = [
@@ -825,7 +827,7 @@ class _FieldDef(NamedTuple):
                     uuid=file_uuid,
                     format_context=dict(
                         format_context,
-                        num=num  # add num to be able to generate
+                        num=num,  # add num to be able to generate
                         # different gcs keys for each multi-artifact file.
                     ),
                 )
@@ -1002,9 +1004,9 @@ class Template:
                     data_schemas[table_name] = process_fields(table_schema)
                 processed_worksheet[section_name] = data_schemas
             elif section_name == "prism_arbitrary_data_merge_pointer":
-                processed_worksheet[
-                    "prism_arbitrary_data_merge_pointer"
-                ] = section_schema
+                processed_worksheet["prism_arbitrary_data_merge_pointer"] = (
+                    section_schema
+                )
 
         return processed_worksheet
 

{nci_cidc_schemas-0.26.29 → nci_cidc_schemas-0.26.32}/cidc_schemas/unprism.py

@@ -1,4 +1,5 @@
 """Tools from extracting information from trial metadata blobs."""
+
 from io import StringIO, BytesIO
 from typing import Callable, Dict, List, NamedTuple, Optional, Union
 

{nci_cidc_schemas-0.26.29 → nci_cidc_schemas-0.26.32/nci_cidc_schemas.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nci_cidc_schemas
-Version: 0.26.29
+Version: 0.26.32
 Summary: The CIDC data model and tools for working with it.
 Home-page: https://github.com/NCI-CIDC/cidc-schemas
 Author: NCI

{nci_cidc_schemas-0.26.29 → nci_cidc_schemas-0.26.32}/nci_cidc_schemas.egg-info/SOURCES.txt

@@ -56,6 +56,7 @@ cidc_schemas/schemas/artifacts/artifact_npx.json
 cidc_schemas/schemas/artifacts/artifact_pdf.json
 cidc_schemas/schemas/artifacts/artifact_png.json
 cidc_schemas/schemas/artifacts/artifact_rcc.json
+cidc_schemas/schemas/artifacts/artifact_rdata.json
 cidc_schemas/schemas/artifacts/artifact_tbi.json
 cidc_schemas/schemas/artifacts/artifact_text.json
 cidc_schemas/schemas/artifacts/artifact_tsv.json
@@ -65,6 +66,7 @@ cidc_schemas/schemas/artifacts/artifact_xlsx.json
 cidc_schemas/schemas/artifacts/artifact_yaml.json
 cidc_schemas/schemas/artifacts/artifact_zip.json
 cidc_schemas/schemas/assays/atacseq_assay.json
+cidc_schemas/schemas/assays/ctdna_analysis.json
 cidc_schemas/schemas/assays/ctdna_assay.json
 cidc_schemas/schemas/assays/cytof_assay.json
 cidc_schemas/schemas/assays/cytof_assay_core.json
@@ -121,6 +123,7 @@ cidc_schemas/schemas/assays/components/ngs/rna/salmon.json
 cidc_schemas/schemas/assays/components/ngs/rna/star.json
 cidc_schemas/schemas/assays/components/ngs/rna/trust4.json
 cidc_schemas/schemas/templates/analyses/atacseq_analysis_template.json
+cidc_schemas/schemas/templates/analyses/ctdna_analysis_template.json
 cidc_schemas/schemas/templates/analyses/cytof_analysis_template.json
 cidc_schemas/schemas/templates/analyses/rna_level1_analysis_template.json
 cidc_schemas/schemas/templates/analyses/tcr_analysis_template.json
@@ -210,6 +213,7 @@ tests/data/schemas/invalid_ref.json
 tests/data/schemas/d1/3.json
 tests/data/schemas/d1/d2/2.json
 tests/data/schemas/target-templates/atacseq_analysis_template.json
+tests/data/schemas/target-templates/ctdna_analysis_template.json
 tests/data/schemas/target-templates/rna_level1_analysis_template.json
 tests/data/schemas/target-templates/wes_analysis_template.json
 tests/data/schemas/target-templates/wes_tumor_only_analysis_template.json

nci_cidc_schemas-0.26.32/tests/data/schemas/target-templates/ctdna_analysis_template.json

@@ -0,0 +1,117 @@
+{
+    "title": "ctDNA analysis template",
+    "description": "ctDNA analysis submission.",
+    "prism_template_root_object_schema": "assays/ctdna_analysis.json",
+    "prism_template_root_object_pointer": "/analysis/ctdna_analysis",
+    "properties": {
+        "worksheets": {
+            "ctDNA 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": "/runs/-",
+                "data_columns": {
+                    "ctDNA Runs": {
+                        "run id": {
+                            "merge_pointer": "/run_id",
+                            "type_ref": "assays/ctdna_analysis.json#definitions/sample_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}/ctdna/{run id}/analysis/error.yaml",
+                                    "type_ref": "assays/components/local_file.json#properties/file_path",
+                                    "is_artifact": 1,
+                                    "allow_empty": true
+                                }
+                            ]
+                        },
+                        "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}/ctdna/{run id}/analysis/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}/ctdna/{run id}/analysis/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/align/{id}/{id}_recalibrated.bam'",
+                                    "merge_pointer": "/tumor/alignment/align_recalibrated",
+                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/recalibrated.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}_recalibrated.bam.bai'",
+                                    "merge_pointer": "/tumor/alignment/align_recalibrated_index",
+                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/recalibrated.bam.bai",
+                                    "type_ref": "assays/components/local_file.json#properties/file_path",
+                                    "is_artifact": 1
+                                },
+                                {
+                                    "parse_through": "lambda id: f'{folder or \"\"}analysis/hlahd/{id}/result/{id}_final.result.txt'",
+                                    "merge_pointer": "/tumor/hla/hla_final_result",
+                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/hla_final_result.txt",
+                                    "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/hla/optitype_result",
+                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/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/hla/xhla_report_hla",
+                                    "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/xhla_report_hla.json",
+                                    "type_ref": "assays/components/local_file.json#properties/file_path",
+                                    "is_artifact": 1
+                                }
+                            ]
+                        },
+                        "comments": {
+                            "type_ref": "assays/ctdna_analysis.json#definitions/sample_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"
+                        }
+                    }
+                }
+            }
+        }
+    }
+}