Aligner BWA typo and Mapping clean paths

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

@@ -6,7 +6,11 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 /**
- * Created by pjvan_thof on 1/16/15.
+ * BWA sampe wrapper
+ *
+ * based on executable verion 0.7.10-r789
+ *
+ * @param root Configurable
  */
 class BwaSampe(val root: Configurable) extends Bwa {
   @Input(doc = "Fastq file R1", required = true)
@@ -39,11 +43,14 @@ class BwaSampe(val root: Configurable) extends Bwa {
   var r: String = _
 
   def cmdLine = required(executable) +
-    required("samse") +
+    required("sampe") +
+    optional("-a", a) +
+    optional("-o", o) +
     optional("-n", n) +
+    optional("-N", N) +
+    optional("-c", c) +
     optional("-f", output) +
     optional("-r", r) +
-    optional("-c", c) +
     conditional(P, "-P") +
     conditional(s, "-s") +
     conditional(A, "-A") +

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

@@ -123,7 +123,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
 
   def biopetScript() {
     if (!skipFlexiprep) {
-      flexiprep.outputDir = outputDir + "flexiprep/"
+      flexiprep.outputDir = outputDir + "flexiprep" + File.separator
       flexiprep.input_R1 = input_R1
       if (paired) flexiprep.input_R2 = input_R2
       flexiprep.sampleId = this.sampleId
@@ -208,7 +208,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
       bamFile = mergeSamFile.output
     }
 
-    if (!skipMetrics) addAll(BamMetrics(this, bamFile, outputDir + "metrics/").functions)
+    if (!skipMetrics) addAll(BamMetrics(this, bamFile, outputDir + "metrics" + File.separator).functions)
 
     add(Ln(this, swapExt(outputDir, bamFile, ".bam", ".bai"), swapExt(outputDir, finalBamFile, ".bam", ".bai")))
     add(Ln(this, bamFile, finalBamFile))
@@ -357,6 +357,4 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
   }
 }
 
-object Mapping extends PipelineCommand {
-
-}
+object Mapping extends PipelineCommand
\ No newline at end of file