Merge branch 'patch-bowtie' into 'develop'

Patch bowtie

Fix error on paired end reads for bowtie

See merge request !106

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

@@ -23,16 +23,16 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Fastq file R1", shortName = "R1")
-  var R1: File = _
+  var R1: File = null
 
   @Input(doc = "Fastq file R2", shortName = "R2", required = false)
-  var R2: File = _
+  var R2: Option[File] = None
 
-  @Input(doc = "The reference file for the bam files.", shortName = "R")
+  @Input(doc = "The reference file for the bam files.", shortName = "R", required = true)
   var reference: File = config("reference")
 
-  @Output(doc = "Output file SAM", shortName = "output")
-  var output: File = _
+  @Output(doc = "Output file SAM", shortName = "output", required = true)
+  var output: File = null
 
   executable = config("exe", default = "bowtie", freeVar = false)
   override val versionRegex = """.*[Vv]ersion:? (.*)""".r
@@ -67,8 +67,13 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
       optional("--maxbts", maxbts) +
       optional("--maqerr", maqerr) +
       required(reference) +
-      required(R1) +
-      optional(R2) +
+      (R2 match {
+        case Some(r2) => {
+          required("-1", R1) +
+            optional("-2", r2)
+        }
+        case _ => required(R1)
+      }) +
       " > " + required(output)
   }
 }
\ No newline at end of file

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

@@ -368,7 +368,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
   def addBowtie(R1: File, R2: File, output: File, deps: List[File]): File = {
     val bowtie = new Bowtie(this)
     bowtie.R1 = R1
-    if (paired) bowtie.R2 = R2
+    if (paired) bowtie.R2 = Some(R2)
     bowtie.deps = deps
     bowtie.output = this.swapExt(output.getParent, output, ".bam", ".sam")
     bowtie.isIntermediate = true

public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

@@ -3,6 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.mapping
 import java.io.File
 
 import com.google.common.io.Files
+import nl.lumc.sasc.biopet.extensions._
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
@@ -12,10 +13,7 @@ import org.testng.annotations.{ AfterClass, DataProvider, Test }
 import nl.lumc.sasc.biopet.core.config.Config
 import nl.lumc.sasc.biopet.extensions.bwa.{ BwaSamse, BwaSampe, BwaAln, BwaMem }
 import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, AddOrReplaceReadGroups, MarkDuplicates, SortSam }
-import nl.lumc.sasc.biopet.extensions._
-import nl.lumc.sasc.biopet.pipelines.flexiprep.Cutadapt
-import nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
-import nl.lumc.sasc.biopet.pipelines.flexiprep._
+import nl.lumc.sasc.biopet.pipelines.flexiprep.{ SeqtkSeq, Cutadapt, Fastqc }
 import nl.lumc.sasc.biopet.tools.{ Seqstat, FastqSync }
 import nl.lumc.sasc.biopet.utils.ConfigUtils