From 539afc8949676e5df6b30b3f350759c392630e94 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 6 Jun 2014 12:06:42 +0200
Subject: [PATCH] Changed native linking
---
.../nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index a06465661..7eccc0230 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -188,12 +188,14 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
}
if (!config.getAsBoolean("skip_native_link", false)) {
- val lnR1 = new Ln(config) { this.in = R1 }
+ val lnR1 = new Ln(config)
+ lnR1.in = R1
R1 = new File(outputDir + R1_name + ".qc" + R1_ext)
lnR1.out = R1
add(lnR1)
if (paired) {
- val lnR2 = new Ln(config) { this.in = R2 }
+ val lnR2 = new Ln(config)
+ lnR2.in = R2
R2 = new File(outputDir + R2_name + ".qc" + R2_ext)
lnR2.out = R2
add(lnR2)
--
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