Merge pull request #167 from biopet/fix-BIOPET-755

Small fixes for Gentrap

biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/RefflatStats.scala

@@ -44,6 +44,8 @@ class RefflatStats(val parent: Configurable) extends ToolCommandFunction with Re
   @Output(required = true)
   var intronOutput: File = _
 
+  override def defaultCoreMemory = 5.0
+
   override def beforeGraph(): Unit = {
     super.beforeGraph()
     if (reference == null) reference = referenceFasta()

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")
 
+  private def 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") 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") 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") 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") 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"
   }

gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala

@@ -54,7 +54,7 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
     require(bamFiles.nonEmpty)
   }
 
-  lazy val mergeCountFiles: Boolean = config("merge_count_files", default = true)
+  lazy val mergeCountFiles: Boolean = config("merge_count_files", default = bamFiles.size > 1)
 
   private var extraSummaryFiles: Map[String, File] = Map()