Fix wrong threads setting in Bowtie and Bwa wrappers

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

@@ -61,7 +61,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
   /** return commandline to execute */
   def cmdLine = {
     required(executable) +
-      optional("--threads", nCoresRequest) +
+      optional("--threads", threads) +
       conditional(sam, "--sam") +
       conditional(best, "--best") +
       conditional(strata, "--strata") +

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

@@ -51,6 +51,7 @@ class BwaAln(val root: Configurable) extends Bwa {
   /** Returns command to execute */
   def cmdLine = required(executable) +
     required("aln") +
+    optional("-t", threads) +
     optional("-n", n) +
     optional("-o", o) +
     optional("-e", e) +

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

@@ -77,7 +77,7 @@ class BwaMem(val root: Configurable) extends Bwa {
       required("mem") +
       optional("-k", k) +
       optional("-r", r) +
-      optional("-t", nCoresRequest) +
+      optional("-t", threads) +
       optional("-R", R) +
       conditional(M, "-M") +
       conditional(S, "-S") +