Update WES-analysis files (#281)

* remove *.sorted.bam files * add wes_version report file * bump schemas __version__ = '0.15.5' * update docs
CIMAC-CIDC · Jan 29, 2020 · b38726b · b38726b
1 parent 3c5043b
commit b38726b
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Showing 23 changed files with 3,197 additions and 6,685 deletions.
diff --git a/cidc_schemas/__init__.py b/cidc_schemas/__init__.py
@@ -4,4 +4,4 @@
 
 __author__ = """James Lindsay"""
 __email__ = "jlindsay@jimmy.harvard.edu"
-__version__ = "0.15.4"
+__version__ = "0.15.5"
diff --git a/cidc_schemas/schemas/assays/components/ngs/wes/alignment.json b/cidc_schemas/schemas/assays/components/ngs/wes/alignment.json
@@ -11,12 +11,6 @@
     "align_recalibrated_index": {
       "$ref": "artifacts/artifact_bam_bai.json"
     },
-    "align_sorted": {
-      "$ref": "artifacts/artifact_bam.json"
-    },
-    "align_sorted_index": {
-      "$ref": "artifacts/artifact_bam_bai.json"
-    },
     "align_sorted_dedup": {
       "$ref": "artifacts/artifact_bam.json"
     },
@@ -27,8 +21,6 @@
   "required": [
     "align_recalibrated",
     "align_recalibrated_index",
-    "align_sorted",
-    "align_sorted_index",
     "align_sorted_dedup",
     "align_sorted_dedup_index"
   ],

diff --git a/cidc_schemas/schemas/assays/components/ngs/wes/report.json b/cidc_schemas/schemas/assays/components/ngs/wes/report.json
@@ -0,0 +1,16 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "$id": "report",
+  "title": "WES Pipeline Version",
+  "type": "object",
+  "description": "WES pipeline version/commit string.",
+  "properties": {
+    "wes_version": {
+      "$ref": "artifacts/artifact_text.json"
+    }
+  },
+  "required": [
+  "wes_version"
+  ],
+  "additionalProperties": false
+}
diff --git a/cidc_schemas/schemas/assays/components/ngs/wes/wes_pair_analysis.json b/cidc_schemas/schemas/assays/components/ngs/wes/wes_pair_analysis.json
@@ -36,6 +36,9 @@
     },
     "corealignments": {
       "$ref": "assays/components/ngs/wes/corealignments.json"
+    },
+    "report": {
+      "$ref": "assays/components/ngs/wes/report.json"
     }
   },
   "required": [

diff --git a/cidc_schemas/schemas/templates/analyses/wes_analysis_template.json b/cidc_schemas/schemas/templates/analyses/wes_analysis_template.json
@@ -155,27 +155,20 @@
                                     "gcs_uri_format": "{protocol identifier}/{run id}/wes_analysis/all_summaries.txt",
                                     "type_ref": "assays/components/local_file.json#properties/file_path",
                                     "is_artifact": 1
+                                },
+                                {
+                                    "parse_through": "lambda id: f'analysis/report/wes_version.txt'",
+                                    "merge_pointer": "/report/wes_version",
+                                    "gcs_uri_format": "{protocol identifier}/{run id}/wes_analysis/wes_version.txt",
+                                    "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'analysis/align/{id}/{id}.sorted.bam'",
-                                    "merge_pointer": "/tumor/alignment/align_sorted",
-                                    "gcs_uri_format": "{protocol identifier}/{run id}/wes_analysis/tumor/{tumor cimac id}/sorted.bam",
-                                    "type_ref": "assays/components/local_file.json#properties/file_path",
-                                    "is_artifact": 1
-                                },
-                                {
-                                    "parse_through": "lambda id: f'analysis/align/{id}/{id}.sorted.bam.bai'",
-                                    "merge_pointer": "/tumor/alignment/align_sorted_index",
-                                    "gcs_uri_format": "{protocol identifier}/{run id}/wes_analysis/tumor/{tumor cimac id}/sorted.bam.bai",
-                                    "type_ref": "assays/components/local_file.json#properties/file_path",
-                                    "is_artifact": 1
-                                },
                                 {
                                     "parse_through": "lambda id: f'analysis/align/{id}/{id}_recalibrated.bam'",
                                     "merge_pointer": "/tumor/alignment/align_recalibrated",
@@ -273,20 +266,6 @@
                             "merge_pointer": "/normal/cimac_id",
                             "type_ref": "sample.json#properties/cimac_id",
                             "process_as": [
-                                {
-                                    "parse_through": "lambda id: f'analysis/align/{id}/{id}.sorted.bam'",
-                                    "merge_pointer": "/normal/alignment/align_sorted",
-                                    "gcs_uri_format": "{protocol identifier}/{run id}/wes_analysis/normal/{normal cimac id}/sorted.bam",
-                                    "type_ref": "assays/components/local_file.json#properties/file_path",
-                                    "is_artifact": 1
-                                },
-                                {
-                                    "parse_through": "lambda id: f'analysis/align/{id}/{id}.sorted.bam.bai'",
-                                    "merge_pointer": "/normal/alignment/align_sorted_index",
-                                    "gcs_uri_format": "{protocol identifier}/{run id}/wes_analysis/normal/{normal cimac id}/sorted.bam.bai",
-                                    "type_ref": "assays/components/local_file.json#properties/file_path",
-                                    "is_artifact": 1
-                                },
                                 {
                                     "parse_through": "lambda id: f'analysis/align/{id}/{id}_recalibrated.bam'",
                                     "merge_pointer": "/normal/alignment/align_recalibrated",