From 102aa9e7856163dd4a855faa30221359d276da58 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Fri, 15 Jan 2016 16:49:46 +0100
Subject: [PATCH] Fix output path for pindel (pindel outputs to certain dir
with prefix_)
---
.../nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala | 3 +++
1 file changed, 3 insertions(+)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
index d210b920f..18f4e4606 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
@@ -123,6 +123,9 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
}
}
+ // modify `output_prefix` to include samplename
+ output_prefix = new File(output_prefix + File.separator, "sample" )
+
// set the output file
output_file = new File(output_prefix, "_D")
}
--
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