From 3584a778e4760dda7e3c79948d42d50db9ee7dd8 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 1 Aug 2015 13:52:34 +0200
Subject: [PATCH] Saver execution order
---
.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
index 5eb7bf411..6d790f104 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
@@ -280,9 +280,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
} else None
lazy val svCalling = if (config("sv_calling", default = false).asBoolean) {
- val svCalling = new ShivaSvCalling(this)
- samples.foreach(x => x._2.preProcessBam.foreach(bam => svCalling.addBamFile(bam, Some(x._1))))
- Some(svCalling)
+ Some(new ShivaSvCalling(this))
} else None
/** This will add the mutisample variantcalling */
@@ -298,6 +296,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
svCalling.foreach(sv => {
sv.outputDir = new File(outputDir, "sv_calling")
+ samples.foreach(x => x._2.preProcessBam.foreach(bam => sv.addBamFile(bam, Some(x._1))))
sv.init()
sv.biopetScript()
addAll(sv.functions)
--
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