Merge branch 'fix-BIOPET-317' into 'develop'

Fixing BIOPET-317 See merge request !489

Merge branch 'fix-BIOPET-317' into 'develop'
Fixing BIOPET-317 See merge request !489
7de7e6ee · Sander Bollen · ba0deb1c · 81188921 · 7de7e6ee
Commit 7de7e6ee authored Dec 13, 2016 by Sander Bollen
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Showing with 6 additions and 2 deletions

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala ...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala +6 -2

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--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -269,11 +269,15 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
    if (fastq_R1.length > 1) {
      val zcat = new Zcat(this)
      zcat.input = fastq_R1
-      add(zcat | new Gzip(this) > fastqR1Qc)
+      val cmdR1 = zcat | new Gzip(this) > fastqR1Qc
+      cmdR1.isIntermediate = !keepQcFastqFiles
+      add(cmdR1)
      if (paired) {
        val zcat = new Zcat(this)
        zcat.input = fastq_R2
-        add(zcat | new Gzip(this) > fastqR2Qc.get)
+        val cmdR2 = zcat | new Gzip(this) > fastqR2Qc.get
+        cmdR2.isIntermediate = !keepQcFastqFiles
+        add(cmdR2)
      }
    }