Merge remote-tracking branch 'remotes/origin/fix-mapping' into feature-parralel_mapping_tests

25cc88c4 · Peter van 't Hof · 9cae1c11 · 55c9af30 · 25cc88c4
Commit 25cc88c4 authored Oct 16, 2015 by Peter van 't Hof
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -141,8 +141,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S

    paired = input_R2.isDefined

-    if (readgroupId == null) readgroupId = sampleId.get + "-" + libId.get
-    else if (readgroupId == null) readgroupId = config("readgroup_id")
+    if (readgroupId == null)
+      readgroupId = config("readgroup_id", default = sampleId.get + "-" + libId.get)

    if (outputName == null) outputName = readgroupId