Fixing job script

0d996e40 · pjvan_thof · dda90b04 · 0d996e40 · 677d7574 · a30ff57a
Commit 0d996e40 authored Apr 20, 2017 by pjvan_thof
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala .../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala +1 -1

gatk gatk +1 -1

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--- a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
@@ -54,7 +54,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
    }
    writer.println("set -eubf")
    writer.println("set -o pipefail")
-    writer.println(this.commandLine)
+    writer.println(lines.mkString("\n"))
    jobDelayTime.foreach(x => writer.println(s"sleep $x"))
    writer.close()
  }

--- a/gatk @ 677d7574
+++ b/gatk @ 677d7574
-Subproject commit a30ff57a56bee919a619190d43f22d3b8f9ef8d7
+Subproject commit 677d757419f515779766b10149b0e92eff71e5b2