Merge branch 'fix-BIOPET-412' into 'develop'

Fix BIOPET-412

Fix BIOPET-412

See merge request !487

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

@@ -57,7 +57,7 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
     for (q <- qscript.summaryQScripts)
       deps :+= q.summaryFile
     for ((_, l) <- qscript.summarizables; s <- l) s match {
-      case f: QFunction => try {
+      case f: QFunction if qscript.functions.contains(f) => try {
         deps :+= f.firstOutput
       } catch {
         case e: NullPointerException => logger.warn("Queue values are not init")

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

@@ -54,12 +54,14 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
     swapExt(outputDir, flash.notCombinedR2, ".fastq.gz", ".clip.fastq.gz")
   else flash.notCombinedR2
 
+  val keepFastaqFiles: Boolean = config("keep_fastq_files", default = false)
+
   /** Pipeline itself */
   def biopetScript(): Unit = {
     flash.outputDirectory = new File(outputDir, "flash")
     flash.fastqR1 = fastqR1
     flash.fastqR2 = fastqR2
-    flash.isIntermediate = (forwardPrimers ::: reversePrimers).nonEmpty
+    flash.isIntermediate = !keepFastaqFiles || (forwardPrimers ::: reversePrimers).nonEmpty
     add(flash)
 
     if ((forwardPrimers ::: reversePrimers).nonEmpty) {
@@ -67,6 +69,7 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
       cutadapt.fastqInput = flash.combinedFastq
       cutadapt.fastqOutput = this.combinedFastq
       cutadapt.statsOutput = swapExt(outputDir, cutadapt.fastqOutput, ".fastq.gz", ".stats")
+      cutadapt.isIntermediate = !keepFastaqFiles
       (forwardPrimers ::: reversePrimers).foreach(cutadapt.anywhere += _)
       add(cutadapt)
       addSummarizable(cutadapt, "cutadapt")

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

@@ -58,6 +58,7 @@ class GearsQiimeClosed(val root: Configurable) extends QScript with SummaryQScri
     splitLib.input :+= fastqInput
     splitLib.outputDir = new File(outputDir, "split_libraries_fastq")
     sampleId.foreach(splitLib.sampleIds :+= _.replaceAll("_", "-"))
+    splitLib.isIntermediate = true
     add(splitLib)
 
     val closedReference = new PickClosedReferenceOtus(this)

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

@@ -51,6 +51,7 @@ class GearsQiimeOpen(val root: Configurable) extends QScript with SummaryQScript
     splitLib.input :+= fastqInput
     splitLib.outputDir = new File(outputDir, "split_libraries_fastq")
     sampleId.foreach(splitLib.sampleIds :+= _.replaceAll("_", "-"))
+    splitLib.isIntermediate = true
     add(splitLib)
 
     val openReference = new PickOpenReferenceOtus(this)