Added intermendiate tags

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)

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

@@ -19,11 +19,11 @@ import java.util.Date
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie, Bowtie2}
-import nl.lumc.sasc.biopet.extensions.bwa.{BwaAln, BwaMem, BwaSampe, BwaSamse}
+import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie, Bowtie2 }
+import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
 import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
 import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
-import nl.lumc.sasc.biopet.extensions.picard.{AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam}
+import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam }
 import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
 import nl.lumc.sasc.biopet.extensions._
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics