From 25cffcfa6df0c6cae5244c12251ec4b2c90ad333 Mon Sep 17 00:00:00 2001
From: pjvan_thof <pjrvanthof@gmail.com>
Date: Tue, 12 Jun 2018 12:15:02 +0200
Subject: [PATCH] Added back toolJar as optional

---
 biopet.wdl | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/biopet.wdl b/biopet.wdl
index b9969b8..ea8d2ba 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -169,6 +169,7 @@ task FastqSync {
 }
 
 task SampleConfig {
+    File? toolJar
     String? preCommand
     Array[File]+ inputFiles
     String keyFilePath
@@ -182,11 +183,15 @@ task SampleConfig {
     Float? memoryMultiplier
     Int mem = ceil(select_first([memory, 4.0]))
 
+    String toolCommand = if defined(toolJar)
+    then "java -Xmx" + mem + "G -jar " +toolJar
+    else "biopet-extractadaptersfastqc -Xmx" + mem + "G"
+
     command {
         set -e -o pipefail
         ${preCommand}
         mkdir -p . ${"$(dirname " + jsonOutputPath + ")"} ${"$(dirname " + tsvOutputPath + ")"}
-        biopet-sampleconfig -Xmx${mem}G \
+        ${toolCommand} \
         -i ${sep="-i " inputFiles} \
         ${"--sample " + sample} \
         ${"--library " + library} \
-- 
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