From 3e1bc47a8661bdaf52cce43dfa144b26e77e916b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 13 Feb 2015 13:22:48 +0100
Subject: [PATCH] Added default aligner
---
.../main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index 578f3afc7..19973c3e1 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
@@ -38,7 +38,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
def this() = this(null)
override def defaults = ConfigUtils.mergeMaps(Map(
- "mapping" -> Map("skip_markduplicates" -> true)
+ "mapping" -> Map("skip_markduplicates" -> true, "aligner" -> "bwa")
), super.defaults)
def makeSample(id: String) = new Sample(id)
--
GitLab