Merge pull request #156 from biopet/fix-BIOPET-741

Fixing grouping in GenotypeGVCFs

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/GenotypeGvcfs.scala

@@ -55,7 +55,7 @@ class GenotypeGvcfs(val parent: Configurable) extends QScript with BiopetQScript
     job.out = outputFile
     job.isIntermediate = group.nonEmpty
     val subJobs: ListBuffer[CombineJob] = ListBuffer()
-    val groupedInput = makeEqualGroups(allInput)
+    val groupedInput: List[List[File]] = makeEqualGroups(allInput)
     if (groupedInput.size == 1) job.variant = groupedInput.head
     else {
       for ((list, i) <- groupedInput.zipWithIndex) {
@@ -71,7 +71,7 @@ class GenotypeGvcfs(val parent: Configurable) extends QScript with BiopetQScript
       val groupSize = if (files.size > (maxNumberOfFiles * maxNumberOfFiles)) {
         files.size / maxNumberOfFiles
       } else if (files.size < maxNumberOfFiles) files.size
-      else files.size / (files.size / maxNumberOfFiles)
+      else (files.size.toDouble / (files.size.toDouble / maxNumberOfFiles).ceil).ceil.toInt
       files.grouped(groupSize).toList
     }