Remove unused vars

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -132,7 +132,7 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
     var results: Map[String, File] = Map()
 
     var R1: File = new File(R1_in)
-    var R2: File = new File(R2_in)
+    var R2: File = if (paired) new File(R2_in) else null
     var deps: List[File] = if (paired) List(R1, R2) else List(R1)
 
     val seqtkSeq_R1 = SeqtkSeq(this, R1, swapExt(outDir, R1, R1_ext, ".sanger" + R1_ext), fastqc_R1)
@@ -199,7 +199,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
       }
       sickle.output_stats = swapExt(outDir, R1, R1_ext, ".trim.stats")
       sickle.deps = deps
-      add(sickle, isIntermediate = true)
+      sickle.isIntermediate = true
+      add(sickle)
       summary.addSickle(sickle, chunk)
       R1 = sickle.output_R1
       if (paired) R2 = sickle.output_R2
@@ -256,7 +257,8 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
   }
 
   def extractIfNeeded(file: File, runDir: String): File = {
-    if (file.getName().endsWith(".gz") || file.getName().endsWith(".gzip")) {
+    if (file == null) return file
+    else if (file.getName().endsWith(".gz") || file.getName().endsWith(".gzip")) {
       var newFile: File = swapExt(runDir, file, ".gz", "")
       if (file.getName().endsWith(".gzip")) newFile = swapExt(runDir, file, ".gzip", "")
       val zcatCommand = Zcat(this, file, newFile)

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

@@ -122,12 +122,10 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
   }
 
   def biopetScript() {
-    var fastq_R1: File = input_R1
-    var fastq_R2: File = if (paired) input_R2 else ""
     if (!skipFlexiprep) {
       flexiprep.outputDir = outputDir + "flexiprep/"
-      flexiprep.input_R1 = fastq_R1
-      if (paired) flexiprep.input_R2 = fastq_R2
+      flexiprep.input_R1 = input_R1
+      if (paired) flexiprep.input_R2 = input_R2
       flexiprep.sampleName = this.RGSM
       flexiprep.libraryName = this.RGLB
       flexiprep.init
@@ -145,22 +143,22 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
     var chunks: Map[String, (String, String)] = Map()
     if (chunking) for (t <- 1 to numberChunks.getOrElse(1)) {
       val chunkDir = outputDir + "chunks/" + t + "/"
-      chunks += (chunkDir -> (removeGz(chunkDir + fastq_R1.getName),
-        if (paired) removeGz(chunkDir + fastq_R2.getName) else ""))
+      chunks += (chunkDir -> (removeGz(chunkDir + input_R1.getName),
+        if (paired) removeGz(chunkDir + input_R2.getName) else ""))
     }
-    else chunks += (outputDir -> (flexiprep.extractIfNeeded(fastq_R1, flexiprep.outputDir),
-      flexiprep.extractIfNeeded(fastq_R2, flexiprep.outputDir)))
+    else chunks += (outputDir -> (flexiprep.extractIfNeeded(input_R1, flexiprep.outputDir),
+      flexiprep.extractIfNeeded(input_R2, flexiprep.outputDir)))
 
     if (chunking) {
       val fastSplitter_R1 = new FastqSplitter(this)
-      fastSplitter_R1.input = fastq_R1
+      fastSplitter_R1.input = input_R1
       for ((chunkDir, fastqfile) <- chunks) fastSplitter_R1.output :+= fastqfile._1
       fastSplitter_R1.isIntermediate = true
       add(fastSplitter_R1)
 
       if (paired) {
         val fastSplitter_R2 = new FastqSplitter(this)
-        fastSplitter_R2.input = fastq_R2
+        fastSplitter_R2.input = input_R2
         for ((chunkDir, fastqfile) <- chunks) fastSplitter_R2.output :+= fastqfile._2
         fastSplitter_R2.isIntermediate = true
         add(fastSplitter_R2)