Added a check on empty files

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -19,11 +19,11 @@ import java.util.Date
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie, Bowtie2 }
-import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
+import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie, Bowtie2}
+import nl.lumc.sasc.biopet.extensions.bwa.{BwaAln, BwaMem, BwaSampe, BwaSamse}
 import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
 import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
-import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam }
+import nl.lumc.sasc.biopet.extensions.picard.{AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam}
 import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
 import nl.lumc.sasc.biopet.extensions._
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
@@ -31,7 +31,7 @@ import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
 import nl.lumc.sasc.biopet.pipelines.gears.GearsSingle
 import nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
-import nl.lumc.sasc.biopet.utils.textToSize
+import nl.lumc.sasc.biopet.utils.{Logging, textToSize}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
@@ -150,9 +150,11 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
   /** Will be executed before script */
   def init() {
     require(outputDir != null, "Missing output directory on mapping module")
-    require(inputR1 != null, "Missing output directory on mapping module")
+    require(inputR1 != null, "Missing inputR1 on mapping module")
     require(sampleId.isDefined, "Missing sample ID on mapping module")
     require(libId.isDefined, "Missing library ID on mapping module")
+    if (inputR1.exists() && inputR1.length() == 0) Logging.addError(s"Input R1 is a empty file: $inputR1")
+    inputR2.foreach(r => if (r.exists() && r.length() == 0) Logging.addError(s"Input R2 is a empty file: $r"))
 
     inputFiles :+= new InputFile(inputR1)
     inputR2.foreach(inputFiles :+= new InputFile(_))