Change fastq to intermediate

dc0495a6 · pjvan_thof · 9b1ebb8b · dc0495a6
Commit dc0495a6 authored May 09, 2017 by pjvan_thof
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gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala ...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala +3 -1

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--- a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
+++ b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
@@ -123,7 +123,9 @@ class GearsSingle(val parent: Configurable)
      if (r1.size == 1) r1.head
      else {
        val outputFile = new File(outputDir, "merged.R1.fq.gz")
-        add(Zcat(this, r1) | new Gzip(this) > outputFile)
+        val merge = Zcat(this, r1) | new Gzip(this) > outputFile
+        merge.isIntermediate = true
+        add(merge)
        outputFile
      }