From 52a6e6b1d1fc7ae98332753447b8bf0afd540f76 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 17 May 2018 09:56:50 +0200
Subject: [PATCH] use stdout() and fix regex
---
biopet.wdl | 6 ++----
gatk.wdl | 2 +-
2 files changed, 3 insertions(+), 5 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index 6c9f68c..93dab22 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -60,7 +60,6 @@ task SampleConfig {
String? preCommand
String tool_jar
Array[File]+ inputFiles
- String stdoutFile
String? sample
String? library
String? readgroup
@@ -81,12 +80,11 @@ task SampleConfig {
${"--library " + library} \
${"--readgroup " + readgroup} \
${"--jsonOutput " + jsonOutputPath} \
- ${"--tsvOutput " + tsvOutputPath} \
- > ${stdoutFile}
+ ${"--tsvOutput " + tsvOutputPath}
}
output {
- File keysFile = stdoutFile
+ File keysFile = stdout()
File? jsonOutput = jsonOutputPath
File? tsvOutput = tsvOutputPath
}
diff --git a/gatk.wdl b/gatk.wdl
index 56e2bd4..bd97b42 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -278,7 +278,7 @@ task SplitNCigarReads {
output {
File bam = output_bam
- File bam_index = sub(output_bam, ".bam$", ".bai")
+ File bam_index = sub(output_bam, "\\.bam$", ".bai")
}
runtime {
--
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