Fixing Ln

8a0e0c8e · Peter van 't Hof · dd6b452a · 8a0e0c8e
Commit 8a0e0c8e authored Apr 14, 2017 by Peter van 't Hof
--- a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
@@ -271,7 +271,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
            add(merge)
          }
          add(SambambaMarkdup(qscript, mergedBam, bamFile.get, isIntermediate = !keepMergedFiles))
-          Ln(qscript, bamFile.get + ".bai", bamFile.get.getAbsolutePath.stripSuffix(".bam") + ".bai")
+          add(Ln(qscript, bamFile.get + ".bai", bamFile.get.getAbsolutePath.stripSuffix(".bam") + ".bai"))
        case _ => throw new IllegalStateException("This should not be possible, unimplemented MergeStrategy?")
      }