Merge branch 'develop' into feature-scoverage

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

@@ -153,11 +153,11 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
           scriptOutput.rawVcfFile = m2v.output
 
           val vcfFilter = new VcfFilter(this) {
-            override def defaults = ConfigUtils.mergeMaps(Map("min_sample_depth" -> 8,
+            override def defaults = Map("min_sample_depth" -> 8,
               "min_alternate_depth" -> 2,
               "min_samples_pass" -> 1,
               "filter_ref_calls" -> true
-            ), super.defaults)
+            )
           }
           vcfFilter.inputVcf = m2v.output
           vcfFilter.outputVcf = swapExt(outputDir, m2v.output, ".vcf", ".filter.vcf.gz")

public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala

@@ -35,10 +35,10 @@ trait BastyTrait extends MultiSampleQScript {
 
   def variantcallers = List("freebayes")
 
-  override def defaults = ConfigUtils.mergeMaps(Map(
+  override def defaults = Map(
     "ploidy" -> 1,
     "variantcallers" -> variantcallers
-  ), super.defaults)
+  )
 
   lazy val shiva: ShivaTrait = new Shiva(qscript)
 

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala → public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala

@@ -47,7 +47,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
   override def defaultCoreMemory = 4.0
   override def defaultThreads = 8
 
-  var sam: Boolean = config("sam", default = true)
+  var sam: Boolean = config("sam", default = false)
   var sam_RG: Option[String] = config("sam-RG")
   var seedlen: Option[Int] = config("seedlen")
   var seedmms: Option[Int] = config("seedmms")