From 7e142153a58c63430f3d6bdb9d0b03b73d685254 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Mon, 14 May 2018 11:59:34 +0200
Subject: [PATCH] stdout to file
---
biopet.wdl | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index 89293a9..6c9f68c 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -60,6 +60,7 @@ task SampleConfig {
String? preCommand
String tool_jar
Array[File]+ inputFiles
+ String stdoutFile
String? sample
String? library
String? readgroup
@@ -80,14 +81,14 @@ task SampleConfig {
${"--library " + library} \
${"--readgroup " + readgroup} \
${"--jsonOutput " + jsonOutputPath} \
- ${"--tsvOutput " + tsvOutputPath}
+ ${"--tsvOutput " + tsvOutputPath} \
+ > ${stdoutFile}
}
output {
- Array[String] keys = read_lines(stdout())
+ File keysFile = stdoutFile
File? jsonOutput = jsonOutputPath
File? tsvOutput = tsvOutputPath
- Object values = if (defined(tsvOutput) && size(tsvOutput) > 0) then read_map(tsvOutput) else { "": "" }
}
runtime {
--
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