Merge pull request #82 from biopet/Fix-BIOPET-572

Change default file name from "R1" to "sampleName - libName"

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala

@@ -56,12 +56,7 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript
     if (sampleId == null || sampleId == None) Logging.addError("Missing sample ID on GearsSingle module")
 
     if (outputName == null) {
-      if (fastqR1.nonEmpty) outputName = fastqR1.headOption.map(_.getName
-        .stripSuffix(".gz")
-        .stripSuffix(".fastq")
-        .stripSuffix(".fq"))
-        .getOrElse("noName")
-      else outputName = bamFile.map(_.getName.stripSuffix(".bam")).getOrElse("noName")
+      outputName = sampleId.getOrElse("noName") + libId.map("-" + _).getOrElse("")
     }
 
     if (fastqR1.nonEmpty) {

gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala

@@ -108,7 +108,7 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
         gears.outputName shouldBe "test"
       } else {
         // in the following cases the filename should have been determined by the filename
-        gears.outputName shouldBe (if (inputMode == Some("bam")) "bamfile" else "R1")
+        gears.outputName shouldBe "sampleName-libName"
       }
 
       val pipesJobs = gears.functions.filter(_.isInstanceOf[BiopetCommandLineFunction])