Adding default gtf file to STAR

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala

@@ -80,8 +80,13 @@ class Star(val parent: Configurable)
   var genomeSAindexNbases: Option[Long] = config("genomesaindexnbases")
   var genomeSAsparseD: Option[Int] = config("genomesasparsed")
 
+  val defaultGtf: Option[File] = config("annotation_gtf")
   @Input(required = false)
-  var sjdbGTFfile: Option[File] = config("sjdbgtfile")
+  var sjdbGTFfile: Option[File] = defaultGtf match {
+    case Some(file) => config("sjdbgtfile", default = file)
+    case _ => config("sjdbgtfile")
+  }
+
   var sjdbGTFchrPrefix: Option[String] = config("sjdbgtfchrprefix")
   var sjdbGTFfeatureExon: Option[String] = config("sjdbgtffeatureexon")
   var sjdbGTFtagExonParentTranscript: Option[String] = config("sjdbgtftagexonparenttranscript")

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateAnnotation.scala

@@ -31,16 +31,17 @@ object ValidateAnnotation extends ToolCommand {
                   gtfFiles: List[File] = Nil)
 
   class OptParser extends AbstractOptParser[Args](commandName) {
-    opt[File]('r', "refflatFile") unbounded() maxOccurs 1 valueName "<file>" action { (x, c) =>
+    opt[File]('r', "refflatFile") unbounded () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(refflatFile = Some(x))
     } text "Refflat file to check"
-    opt[File]('g', "gtfFile") unbounded() valueName "<file>" action { (x, c) =>
+    opt[File]('g', "gtfFile") unbounded () valueName "<file>" action { (x, c) =>
       c.copy(gtfFiles = x :: c.gtfFiles)
     } text "Gtf files to check"
-    opt[File]('R', "reference") unbounded() required () maxOccurs 1 valueName "<file>" action { (x, c) =>
-      c.copy(reference = x)
+    opt[File]('R', "reference") unbounded () required () maxOccurs 1 valueName "<file>" action {
+      (x, c) =>
+        c.copy(reference = x)
     } text "Reference fasta to check vcf file against"
-    opt[Unit]("disableFail") unbounded() maxOccurs 1 valueName "<file>" action { (_, c) =>
+    opt[Unit]("disableFail") unbounded () maxOccurs 1 valueName "<file>" action { (_, c) =>
       c.copy(failOnError = false)
     } text "Do not fail on error. The tool will still exit when encountering an error, but will do so with exit code 0"
   }