add qcFaield field to the case_detailed_summmary format

changes/add_qcFailed_detailed_cases.md

@@ -0,0 +1 @@
+qcFailed field to the case_detailed_summary input format

plugin-cardea/src/main/java/ca/on/oicr/gsi/shesmu/cardea/LimsSequencingInfo.java

@@ -5,11 +5,13 @@
 public class LimsSequencingInfo {
   private final String id;
   private final boolean supplemental;
+  private final boolean qcFailed;
 
-  public LimsSequencingInfo(String id, boolean supplemental) {
+  public LimsSequencingInfo(String id, boolean supplemental, boolean qcFailed) {
     super();
     this.id = id;
     this.supplemental = supplemental;
+    this.qcFailed = qcFailed;
   }
 
   @ShesmuVariable
@@ -21,4 +23,9 @@ public String id() {
   public boolean supplemental() {
     return supplemental;
   }
+
+  @ShesmuVariable
+  public boolean qcFailed() {
+    return qcFailed;
+  }
 }

plugin-cardea/src/main/java/ca/on/oicr/gsi/shesmu/cardea/SequencingTestValue.java

@@ -18,7 +18,9 @@ public SequencingTestValue(
     this.test = test;
     this.type = type;
     this.limsIds =
-        limsIds.map(info -> new Tuple(info.id(), info.supplemental())).collect(Collectors.toSet());
+        limsIds
+            .map(info -> new Tuple(info.id(), info.supplemental(), info.qcFailed()))
+            .collect(Collectors.toSet());
     this.complete = complete;
   }