Adding missing output files

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -228,6 +228,7 @@ class Flexiprep(val parent: Configurable) extends QScript with SummaryQScript wi
         override def summaryDeps: List[File] = qcCmdR1.summaryDeps ::: qcCmdR2.summaryDeps ::: super.summaryDeps
       }
 
+      pipe.jobOutputFile = new File(outDir, ".qc_cmd.out")
       pipe.deps ::= fastqcR1.output
       pipe.deps ::= fastqcR2.output
       pipe.deps ::= R1_in
@@ -243,6 +244,7 @@ class Flexiprep(val parent: Configurable) extends QScript with SummaryQScript wi
       R2 = Some(fqSync.outputFastq2)
     } else {
       qcCmdR1.nCoresRequest = Some(2)
+      qcCmdR1.jobOutputFile = new File(outDir, ".qc_cmd.out")
       add(qcCmdR1)
       R1 = qcCmdR1.output
     }