Fixing gears merge step

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

@@ -84,13 +84,13 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
   protected def executeFlexiprep(r1: List[File], r2: List[File]): (File, Option[File]) = {
     val read1: File = if (r1.size == 1) r1.head else {
       val outputFile = new File(outputDir, "merged.R1.fq.gz")
-      Zcat(this, r1) | new Gzip(this) > outputFile
+      add(Zcat(this, r1) | new Gzip(this) > outputFile)
       outputFile
     }
 
     val read2: Option[File] = if (r2.size <= 1) r2.headOption else {
       val outputFile = new File(outputDir, "merged.R2.fq.gz")
-      Zcat(this, r2) | new Gzip(this) > outputFile
+      add(Zcat(this, r2) | new Gzip(this) > outputFile)
       Some(outputFile)
     }
 

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala

@@ -67,7 +67,10 @@ trait MultisampleMappingTrait extends MultiSampleQScript
     Some(report)
   }
 
-  override def defaults: Map[String, Any] = super.defaults ++ Map("reordersam" -> Map("allow_incomplete_dict_concordance" -> true))
+  override def defaults: Map[String, Any] = super.defaults ++ Map(
+    "reordersam" -> Map("allow_incomplete_dict_concordance" -> true),
+    "gears" -> Map("skip_flexiprep" -> true)
+  )
 
   override def fixedValues: Map[String, Any] = super.fixedValues ++ Map("gearssingle" -> Map("skip_flexiprep" -> true))
 
@@ -99,6 +102,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
 
       lazy val inputR1: Option[File] = MultisampleMapping.fileMustBeAbsolute(config("R1"))
       lazy val inputR2: Option[File] = MultisampleMapping.fileMustBeAbsolute(config("R2"))
+      lazy val qcFastqR1 = mapping.map(_.flexiprep.fastqR1Qc)
+      lazy val qcFastqR2 = mapping.flatMap(_.flexiprep.fastqR2Qc)
       lazy val inputBam: Option[File] = MultisampleMapping.fileMustBeAbsolute(if (inputR1.isEmpty) config("bam") else None)
       lazy val bamToFastq: Boolean = config("bam_to_fastq", default = false)
       lazy val correctReadgroups: Boolean = config("correct_readgroups", default = false)
@@ -274,8 +279,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
           add(gears)
         case "all" =>
           val gears = new GearsSingle(qscript)
-          gears.fastqR1 = libraries.flatMap(_._2.inputR1).toList
-          gears.fastqR2 = libraries.flatMap(_._2.inputR2).toList
+          gears.fastqR1 = libraries.flatMap(_._2.qcFastqR1).toList
+          gears.fastqR2 = libraries.flatMap(_._2.qcFastqR2).toList
           gears.sampleId = Some(sampleId)
           gears.outputDir = new File(sampleDir, "gears")
           add(gears)