Formatting updates

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala

@@ -96,8 +96,8 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
     if (output_stats.exists) for (line <- Source.fromFile(output_stats).getLines) {
       line match {
         // single run
-        case sKept(num) => stats += ("num_reads_kept" -> num.toInt)
-        case sDiscarded(num) => stats += ("num_reads_discarded_total" -> num.toInt)
+        case sKept(num)              => stats += ("num_reads_kept" -> num.toInt)
+        case sDiscarded(num)         => stats += ("num_reads_discarded_total" -> num.toInt)
         // paired run
         case pPairKept(reads, pairs) => stats += ("num_reads_kept" -> reads.toInt)
         case pSingleKept(total, r1, r2) => {
@@ -116,8 +116,8 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
     if (stats.contains("num_reads_discarded_both")) {
       stats += ("num_reads_discarded_total" -> {
         stats.getOrElse("num_reads_discarded_R1", 0) + stats.getOrElse("num_reads_discarded_R2", 0) +
-        stats.getOrElse("num_reads_discarded_both", 0)
-        })
+          stats.getOrElse("num_reads_discarded_both", 0)
+      })
     }
 
     stats.toMap

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala

@@ -79,7 +79,7 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
     case None => Map()
     case Some((header, content)) =>
       (for (i <- 0 to header.size if i < content.head.size)
-      yield header(i).toLowerCase -> content.head(i)).toMap
+        yield header(i).toLowerCase -> content.head(i)).toMap
   }
 
   override def commandLine = super.commandLine +

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -90,7 +90,7 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
         "format" -> "sam"
       ),
       // avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
-      "picard" -> Map (
+      "picard" -> Map(
         "programrecordid" -> "null"
       )
     ), super.defaults)
@@ -709,16 +709,17 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
       add(sampleAlnJob)
       // general RNA-seq metrics, if there are > 1 library
       collectRnaSeqMetricsJob match {
-        case Some(j)  => add(j); addSummarizable(j, "rna_metrics")
-        case None     => ;
+        case Some(j) =>
+          add(j); addSummarizable(j, "rna_metrics")
+        case None => ;
       }
       bamMetricsModule match {
-        case Some(m)  =>
+        case Some(m) =>
           m.init()
           m.biopetScript()
           addAll(m.functions)
           addSummaryQScript(m)
-        case None     => ;
+        case None => ;
       }
       // add strand-specific jobs if defined
       alnPlusStrandJobs.foreach(_.addAllJobs())