From dc0495a6bc748541eeebca829095dcdd2a4ca1f1 Mon Sep 17 00:00:00 2001 From: pjvan_thof <pjrvanthof@gmail.com> Date: Tue, 9 May 2017 15:46:23 +0200 Subject: [PATCH] Change fastq to intermediate --- .../nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git 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 index 3a11baa99..aadf3f64b 100644 --- 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 } -- GitLab