Merge branch 'develop' into fix-BIOPET-306

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

@@ -126,17 +126,21 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
       }
     })
 
-    logger.info("Adding report")
-    this match {
-      case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
-        logger.info("Write report is skipped because sample flag is used")
-      case _ => reportClass.foreach { report =>
-        for (f <- functions) f match {
-          case w: WriteSummary => report.deps :+= w.jobOutputFile
-          case _               =>
+    val writeHtmlReport: Boolean = config("write_html_report", default = true)
+
+    if (writeHtmlReport) {
+      logger.info("Adding report")
+      this match {
+        case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
+          logger.info("Write report is skipped because sample flag is used")
+        case _ => reportClass.foreach { report =>
+          for (f <- functions) f match {
+            case w: WriteSummary => report.deps :+= w.jobOutputFile
+            case _               =>
+          }
+          report.jobOutputFile = new File(report.outputDir, ".report.out")
+          add(report)
         }
-        report.jobOutputFile = new File(report.outputDir, ".report.out")
-        add(report)
       }
     }
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala

@@ -33,7 +33,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
   var R2: File = _
 
   @Input(doc = "The reference file for the bam files.", shortName = "R")
-  var reference: File = null
+  var reference: File = _
 
   @Output(doc = "Output file SAM", shortName = "output")
   var output: File = _
@@ -42,7 +42,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
   var k: Option[Int] = config("k")
   var r: Option[Float] = config("r")
   var S: Boolean = config("S", default = false)
-  var M: Boolean = config("M", default = true)
+  var M: Boolean = config("M", default = false)
   var w: Option[Int] = config("w")
   var d: Option[Int] = config("d")
   var c: Option[Int] = config("c")
@@ -75,7 +75,7 @@ class BwaMem(val parent: Configurable) extends Bwa with Reference {
     if (reference == null) reference = referenceFasta()
   }
 
-  def cmdLine = {
+  def cmdLine: String = {
     required(executable) +
       required("mem") +
       optional("-k", k) +

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])