From 7487eba2babe14603822d9d3890a3418d5562040 Mon Sep 17 00:00:00 2001
From: ffinfo <pjrvanthof@gmail.com>
Date: Tue, 21 Aug 2018 11:09:50 +0200
Subject: [PATCH] Fixing read_lines
---
biopet.wdl | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index 335f26d..755fed1 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -97,8 +97,6 @@ task ExtractAdaptersFastqc {
set -e
~{preCommand}
mkdir -p ~{outputDir}
- touch ~{adapterOutputFilePath}
- touch ~{contamsOutputFilePath}
~{toolCommand} \
--inputFile ~{inputFile} \
~{"--adapterOutputFile " + adapterOutputFilePath } \
@@ -113,8 +111,8 @@ task ExtractAdaptersFastqc {
output {
File adapterOutputFile = adapterOutputFilePath
File contamsOutputFile = contamsOutputFilePath
- Array[String] adapterList = read_lines(adapterOutputFilePath)
- Array[String] contamsList = read_lines(contamsOutputFilePath)
+ Array[String] adapterList = read_lines(adapterOutputFile)
+ Array[String] contamsList = read_lines(contamsOutputFile)
}
runtime {
--
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