From 58300734534909b6898157bf8d32e8256a1fab59 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 11 Jun 2018 07:57:41 +0200
Subject: [PATCH] Added conda env

---
 biopet.wdl | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/biopet.wdl b/biopet.wdl
index f9d2a6b..9a7e402 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -121,7 +121,6 @@ task FastqSync {
 
 task SampleConfig {
     String? preCommand
-    String tool_jar
     Array[File]+ inputFiles
     String keyFilePath
     String? sample
@@ -138,7 +137,7 @@ task SampleConfig {
         set -e -o pipefail
         ${preCommand}
         mkdir -p . ${"$(dirname " + jsonOutputPath + ")"} ${"$(dirname " + tsvOutputPath + ")"}
-        java -Xmx${mem}G -jar ${tool_jar} \
+        biopet-sampleconfig -Xmx${mem}G \
         -i ${sep="-i " inputFiles} \
         ${"--sample " + sample} \
         ${"--library " + library} \
-- 
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