From 8af58a0b3a1ba166b2fdc28a33f81459e731aed0 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Fri, 15 Jan 2016 14:54:24 +0100
Subject: [PATCH] Fix input of bams to svcalling tools..
---
.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala | 1 +
1 file changed, 1 insertion(+)
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
index e97dfd526..13772de16 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
@@ -58,6 +58,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
require(callers.nonEmpty, "must select at least 1 SV caller, choices are: " + callersList.map(_.name).mkString(", "))
callers.foreach { caller =>
+ caller.inputBams = inputBams
caller.outputDir = new File(outputDir, caller.name)
add(caller)
}
--
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