From 76d5fdd562d553077a4489193923c0a11e0bb31e Mon Sep 17 00:00:00 2001
From: Nikos Pappas <n.pappas@lumc.nl>
Date: Wed, 11 Jul 2018 11:09:03 +0200
Subject: [PATCH] Added precommand to ExtractAdaptersFastqc task

---
 biopet.wdl | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/biopet.wdl b/biopet.wdl
index 1f04df3..d076fc2 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -73,6 +73,7 @@ task BaseCounter {
 
 task ExtractAdaptersFastqc {
     File? toolJar
+    String? preCommand
     File inputFile
     String outputDir
     String? adapterOutputFilePath = outputDir + "/adapter.list"
@@ -93,6 +94,7 @@ task ExtractAdaptersFastqc {
 
     command {
     set -e
+    ${preCommand}
     mkdir -p ${outputDir}
     ${toolCommand} \
     --inputFile ${inputFile} \
-- 
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