Added deps to constructor

mapping/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Star.scala

@@ -82,20 +82,22 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
 }
 
 object Star {
-  def apply(configurable: Configurable, R1: File, R2: File, outputDir: String, isIntermediate: Boolean = false): Star = {
+  def apply(configurable: Configurable, R1: File, R2: File, outputDir: String, isIntermediate: Boolean = false, deps:List[File] = Nil): Star = {
     val star = new Star(configurable)
     star.R1 = R1
     if (R2 != null) star.R2 = R2
     star.outputDir = outputDir
     star.isIntermediate = isIntermediate
+    star.deps = deps
     star.afterGraph
     return star
   }
 
-  def _2pass(configurable: Configurable, R1: File, R2: File, outputDir: String, isIntermediate: Boolean = false): (File, List[Star]) = {
+  def _2pass(configurable: Configurable, R1: File, R2: File, outputDir: String, isIntermediate: Boolean = false, deps:List[File] = Nil): (File, List[Star]) = {
     val outDir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
     val starCommand_pass1 = Star(configurable, R1, if (R2 != null) R2 else null, outDir + "aln-pass1/")
     starCommand_pass1.isIntermediate = isIntermediate
+    starCommand_pass1.deps = deps
     starCommand_pass1.afterGraph
 
     val starCommand_reindex = new Star(configurable)
@@ -108,6 +110,7 @@ object Star {
     val starCommand_pass2 = Star(configurable, R1, if (R2 != null) R2 else null, outDir + "aln-pass2/")
     starCommand_pass2.genomeDir = starCommand_reindex.outputDir
     starCommand_pass2.isIntermediate = isIntermediate
+    starCommand_pass2.deps = deps
     starCommand_pass2.afterGraph
 
     return (starCommand_pass2.outputSam, List(starCommand_pass1, starCommand_reindex, starCommand_pass2))