From 4842dd5cbc16a9ccc543664ef35930a54213b6c9 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 5 Feb 2015 16:01:48 +0100
Subject: [PATCH] output name is now config value
---
.../nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
index 10036b6bc..8bac4aaf6 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
@@ -50,7 +50,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
def init() {
if (outputName == null && sampleID != null) outputName = sampleID
- else if (outputName == null) outputName = "noname"
+ else if (outputName == null) outputName = config("output_name", default = "noname")
if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
else if (!outputDir.endsWith("/")) outputDir += "/"
--
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