Merge pull request #30 from icgc-argo/variant-call-update

Variant call update
icgc-argo · May 12, 2020 · 32594ed · 32594ed
2 parents 6a38c19 + 437f87d
commit 32594ed
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Showing 4 changed files with 22 additions and 58 deletions.
diff --git a/schemas/qc_metrics.json b/schemas/qc_metrics.json
@@ -13,7 +13,6 @@
             "workflow_name",
             "workflow_short_name",
             "workflow_version",
-            "analysis_tools",
             "genome_build",
             "run_id",
             "inputs"
@@ -22,7 +21,6 @@
         "required": [
           "workflow_name",
           "workflow_version",
-          "analysis_tools",
           "genome_build",
           "run_id",
           "inputs"
@@ -33,14 +31,11 @@
             "properties": {
               "workflow_name": {
                 "type": "string",
-                "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$"
+                "pattern": "^[a-zA-Z][a-zA-Z0-9 _\\-]+[a-zA-Z0-9]+$"
               },
               "workflow_short_name": {
                 "type": "string",
-                "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$"
-              },
-              "analysis_tools": {
-                "const": null
+                "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+[a-zA-Z0-9]+$"
               },
               "genome_build": {
                 "type": "string",

diff --git a/schemas/sequencing_alignment.json b/schemas/sequencing_alignment.json
@@ -14,7 +14,6 @@
           "enum": [
             "workflow_name",
             "workflow_version",
-            "analysis_tools",
             "genome_build",
             "run_id",
             "inputs"
@@ -23,7 +22,6 @@
         "required": [
           "workflow_name",
           "workflow_version",
-          "analysis_tools",
           "genome_build",
           "run_id",
           "inputs"
@@ -34,14 +32,7 @@
             "properties": {
               "workflow_name": {
                 "type": "string",
-                "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$"
-              },
-              "analysis_tools": {
-                "type": ["array", "null"],
-                "items": {
-                  "type": "string",
-                  "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$"
-                }
+                "pattern": "^[a-zA-Z][a-zA-Z0-9 _\\-]+[a-zA-Z0-9]+$"
               },
               "genome_build": {
                 "type": "string",

diff --git a/schemas/variant_calling.json b/schemas/variant_calling.json
@@ -5,8 +5,7 @@
     "required": [
       "workflow",
       "experiment",
-      "variant_class",
-      "variant_type"
+      "variant_class"
     ],
     "properties": {
       "workflow": {
@@ -15,7 +14,6 @@
             "workflow_name",
             "workflow_short_name",
             "workflow_version",
-            "analysis_tools",
             "genome_build",
             "run_id",
             "inputs"
@@ -25,7 +23,6 @@
           "workflow_name",
           "workflow_short_name",
           "workflow_version",
-          "analysis_tools",
           "genome_build",
           "run_id",
           "inputs"
@@ -34,18 +31,11 @@
         "properties": {
           "workflow_name": {
             "type": "string",
-            "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$"
+            "pattern": "^[a-zA-Z][a-zA-Z0-9 _\\-]+[a-zA-Z0-9]+$"
           },
           "workflow_short_name": {
             "type": "string",
-            "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$"
-          },
-          "analysis_tools": {
-            "type": ["array", "null"],
-            "items": {
-              "type": "string",
-              "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$"
-            }
+            "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+[a-zA-Z0-9]+$"
           },
           "genome_build": {
             "type": "string",
@@ -121,26 +111,11 @@
         }
       },
       "variant_class": {
-        "type": "array",
-        "items":{
-          "type": "string",
-          "enum": [
-            "germline",
-            "somatic"
-          ]
-        }
-      },
-      "variant_type": {
-        "type": "array",
-        "items":{
-          "type": "string",
-          "enum": [
-            "snv",
-            "indel",
-            "cnv",
-            "sv"
-          ]
-        }
+        "type": "string",
+        "enum": [
+          "Germline",
+          "Somatic"
+        ]
       }
     }
   }

diff --git a/schemas/variant_calling_supplement.json b/schemas/variant_calling_supplement.json
@@ -4,7 +4,8 @@
     "type": "object",
     "required": [
       "workflow",
-      "experiment"
+      "experiment",
+      "variant_class"
     ],
     "properties": {
       "workflow": {
@@ -13,7 +14,6 @@
             "workflow_name",
             "workflow_short_name",
             "workflow_version",
-            "analysis_tools",
             "genome_build",
             "run_id",
             "inputs"
@@ -23,7 +23,6 @@
           "workflow_name",
           "workflow_short_name",
           "workflow_version",
-          "analysis_tools",
           "genome_build",
           "run_id",
           "inputs"
@@ -32,14 +31,11 @@
         "properties": {
           "workflow_name": {
             "type": "string",
-            "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$"
+            "pattern": "^[a-zA-Z][a-zA-Z0-9 _\\-]+[a-zA-Z0-9]+$"
           },
           "workflow_short_name": {
             "type": "string",
-            "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+$"
-          },
-          "analysis_tools": {
-            "const": null
+            "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+[a-zA-Z0-9]+$"
           },
           "genome_build": {
             "type": "string",
@@ -111,6 +107,13 @@
               "Bisulfite-Seq",
               "ChIP-Seq"
             ]
+          },
+          "variant_class": {
+            "type": "string",
+            "enum": [
+              "Germline",
+              "Somatic"
+            ]
           }
         }
       }