From fc01ad367d4fb8ce2da860b261fc50fcfa782efc Mon Sep 17 00:00:00 2001
From: npappas <N.Pappas@lumc.nl>
Date: Tue, 5 Jun 2018 10:46:48 +0200
Subject: [PATCH] Various style fixes
---
biopet.wdl | 30 ++++++++++++++++--------------
1 file changed, 16 insertions(+), 14 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index f9d2a6b..607de83 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -12,8 +12,8 @@ task BaseCounter {
Float? memory
Float? memoryMultiplier
-
Int mem = ceil(select_first([memory, 12.0]))
+
command {
set -e -o pipefail
mkdir -p ${outputDir}
@@ -72,7 +72,7 @@ task FastqSplitter {
File inputFastq
String outputPath
Int numberChunks
- String tool_jar
+ File toolJar
Array[Int] chunks = range(numberChunks)
command {
@@ -81,7 +81,7 @@ task FastqSplitter {
mkdir -p ${sep=' ' prefix(outputPath + "/chunk_", chunks)}
if [ ${numberChunks} -gt 1 ]; then
SEP="/${basename(inputFastq)} -o "
- java -jar ${tool_jar} -I ${inputFastq} -o ${sep='$SEP' prefix(outputPath + "/chunk_", chunks)}/${basename(inputFastq)}
+ java -jar ${toolJar} -I ${inputFastq} -o ${sep='$SEP' prefix(outputPath + "/chunk_", chunks)}/${basename(inputFastq)}
else
ln -sf ${inputFastq} ${outputPath}/chunk_0/${basename(inputFastq)}
fi
@@ -100,12 +100,13 @@ task FastqSync {
File in2
String out1path
String out2path
- File tool_jar
+ File toolJar
+
command {
set -e -o pipefail
${preCommand}
mkdir -p $(dirname ${out1path}) $(dirname ${out2path})
- java -jar ${tool_jar} \
+ java -jar ${toolJar} \
--in1 ${in1} \
--in2 ${in2} \
--ref1 ${ref1} \
@@ -113,6 +114,7 @@ task FastqSync {
--out1 ${out1path} \
--out2 ${out2path}
}
+
output {
File out1 = out1path
File out2 = out2path
@@ -121,7 +123,7 @@ task FastqSync {
task SampleConfig {
String? preCommand
- String tool_jar
+ File toolJar
Array[File]+ inputFiles
String keyFilePath
String? sample
@@ -132,13 +134,13 @@ task SampleConfig {
Float? memory
Float? memoryMultiplier
-
Int mem = ceil(select_first([memory, 4.0]))
+
command {
set -e -o pipefail
${preCommand}
mkdir -p . ${"$(dirname " + jsonOutputPath + ")"} ${"$(dirname " + tsvOutputPath + ")"}
- java -Xmx${mem}G -jar ${tool_jar} \
+ java -Xmx${mem}G -jar ${toolJar} \
-i ${sep="-i " inputFiles} \
${"--sample " + sample} \
${"--library " + library} \
@@ -161,23 +163,23 @@ task SampleConfig {
task ScatterRegions {
String? preCommand
- File ref_fasta
- File ref_dict
+ File refFasta
+ File refDict
String outputDirPath
- String tool_jar
+ File toolJar
Int? scatterSize
File? regions
Float? memory
Float? memoryMultiplier
-
Int mem = ceil(select_first([memory, 4.0]))
+
command {
set -e -o pipefail
${preCommand}
mkdir -p ${outputDirPath}
- java -Xmx${mem}G -jar ${tool_jar} \
- -R ${ref_fasta} \
+ java -Xmx${mem}G -jar ${toolJar} \
+ -R ${refFasta} \
-o ${outputDirPath} \
${"-s " + scatterSize} \
${"-L " + regions}
--
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