From 9253f307a2a23c13fa1fdfb249792aff3d356e43 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 19 Jun 2018 10:36:54 +0200
Subject: [PATCH] fix review points
---
biopet.wdl | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index 10ba295..286b2e0 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -280,25 +280,25 @@ task Seqstat {
String? preCommand
File? toolJar
File fastq
- String outputFilePath
+ String outputFile
Float? memory
Float? memoryMultiplier
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(toolJar)
- then "java -Xmx" + mem + "G -jar " +toolJar
+ then "java -Xmx" + mem + "G -jar " + toolJar
else "biopet-seqstat -Xmx" + mem + "G"
command {
set -e -o pipefail
${preCommand}
- mkdir -p $(dirname ${outputFilePath})
+ mkdir -p $(dirname ${outputFile})
${toolCommand} \
--fastq ${fastq} \
- --output ${outputFilePath}
+ --output ${outputFile}
}
output {
- File json = outputFilePath
+ File json = outputFile
}
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 2.0]))
--
GitLab