Merge branch 'develop' into fix-BIOPET-649

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

@@ -206,7 +206,9 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
       val foundAdapters = modules.get("Adapter Content").map { x =>
         val header = x.lines.head.split("\t").tail.zipWithIndex
         val lines = x.lines.tail.map(_.split("\t").tail)
-        val found = header.filter(h => lines.exists(x => x(h._2).toFloat > 0)).map(_._1)
+        val found = header
+          .filter(h => lines.exists(x => x(h._2).toFloat > adapterCutoff))
+          .map(_._1)
         adapterSet.filter(x => found.contains(x.name))
       }
 
@@ -214,6 +216,8 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
     } else Set()
   }
 
+  val adapterCutoff: Float = config("adapter_cutoff", default = 0.001)
+
   @Output
   private var outputFiles: List[File] = Nil
 

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala

@@ -36,11 +36,6 @@ class HaplotypeCallerGvcf(val parent: Configurable) extends Variantcaller {
 
   override def fixedValues = Map("haplotypecaller" -> Map("emitRefConfidence" -> "GVCF"))
 
-  override def defaults = Map("haplotypecaller" -> Map(
-    "variant_index_type" -> "LINEAR",
-    "variant_index_parameter" -> 128000)
-  )
-
   def biopetScript() {
     gVcfFiles = for ((sample, inputBam) <- inputBams) yield {
       val hc = gatk.HaplotypeCaller(this, List(inputBam), new File(outputDir, sample + ".gvcf.vcf.gz"))