From 801f813a7c5b8a2e8527338b4727f5572e378aa9 Mon Sep 17 00:00:00 2001
From: npappas <N.Pappas@lumc.nl>
Date: Wed, 9 May 2018 13:10:16 +0200
Subject: [PATCH] Remove capturing log as output
---
flash.wdl | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/flash.wdl b/flash.wdl
index 90c522e..c081d49 100644
--- a/flash.wdl
+++ b/flash.wdl
@@ -4,7 +4,6 @@ task flash {
File inputR2
String outdirPath
String? outPrefix = "flash"
- String? logPath = outdirPath + "/" + outPrefix + ".log"
Int? minOverlap
Int? maxOverlap
Boolean? compress = true
@@ -22,7 +21,7 @@ task flash {
${true="--compress " false="" defined(compress)} \
${"--min-overlap=" + minOverlap} \
${"--max-overlap=" + maxOverlap} \
- ${inputR1} ${inputR2} 2>&1 | tee ${logPath}
+ ${inputR1} ${inputR2}
}
output {
@@ -31,7 +30,6 @@ task flash {
File notCombined2 = outdirPath + "/" + outPrefix + ".notCombined_2.fastq.gz"
File hist = outdirPath + "/" + outPrefix + ".hist"
File histogram = outdirPath + "/" + outPrefix + ".histogram"
- String log = select_first([logPath])
}
runtime {
--
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