From c22edcf3371a135784a5fae5f90e29e6a159ce4f Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Fri, 15 Jan 2016 16:54:00 +0100
Subject: [PATCH] generate dir for varscan
---
.../pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala | 1 +
1 file changed, 1 insertion(+)
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
index c74d7e54d..f838a2234 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
@@ -36,6 +36,7 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
val sampleVcf = new File(outputDir, s"${name}_$sample.vcf.gz")
val sampleFile = new File(outputDir, s"$sample.name.txt")
+ sampleFile.getParentFile.mkdirs()
sampleFile.deleteOnExit()
val writer = new PrintWriter(sampleFile)
writer.println(sample)
--
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