Commit 4fb8a7b6 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub
Browse files

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

Change default file name from "R1" to "sampleName - libName"
parents 0140969c 58d71f66
......@@ -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 =
else outputName =".bam")).getOrElse("noName")
outputName = sampleId.getOrElse("noName") +"-" + _).getOrElse("")
if (fastqR1.nonEmpty) {
......@@ -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])
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