Merge b579c7d into 1f506fd

4dn-dcic · Sep 7, 2020 · 59f993c · 59f993c
2 parents 1f506fd + b579c7d
commit 59f993c
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Showing 3 changed files with 15 additions and 441 deletions.
diff --git a/chalicelib/check_setup.json b/chalicelib/check_setup.json
@@ -1438,18 +1438,6 @@
             }
         }
     },
-    "cgapS3_er_status" : {
-        "title": "d) CGAP pipeline Part III er",
-        "group": "Pipeline checks",
-        "schedule": {
-            "hourly_checks": {
-                "cgapwolf": {
-                    "kwargs": {"primary": true},
-                    "dependencies": []
-                }
-            }
-        }
-    },
     "ingest_vcf_status" : {
         "title": "d) CGAP trigger VCF ingestion",
         "group": "Pipeline checks",

diff --git a/chalicelib/checks/helpers/cgap_utils.py b/chalicelib/checks/helpers/cgap_utils.py
@@ -142,6 +142,15 @@
 }
 
 
+def remove_parents_without_sample(samples_pedigree):
+    individuals = [i['individual'] for i in samples_pedigree]
+    for a_member in samples_pedigree:
+        parents = a_member['parents']
+        new_parents = [i for i in parents if i in individuals]
+        a_member['parents'] = new_parents
+    return samples_pedigree
+
+
 def check_workflow_version(workflows):
     errors = []
     for a_wf in workflows: