From 6b394c91e308006ca2d9ee3df69fe811dcb23134 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 4 Apr 2018 13:54:14 +0200
Subject: [PATCH] runtime adjustments bwa, exractAdapters
---
bwa.wdl | 2 +-
fastqc.wdl | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index 774f932..53c38f0 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -22,7 +22,7 @@ task BwaMem {
File bamFile = outputPath
}
runtime{
- threads: select_first([threads])
+ threads: if defined(threads) then threads else 1
memory: if defined(memory) then memory else 8
}
}
diff --git a/fastqc.wdl b/fastqc.wdl
index d14faf9..7dddd5d 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -65,7 +65,7 @@ task extractAdapters {
command {
set -e
mkdir -p ${outputDir}
- java -Xmx3G -jar ${extractAdaptersFastqcJar} \
+ java -Xmx4G -jar ${extractAdaptersFastqcJar} \
--inputFile ${inputFile} \
${"--adapterOutputFile " + adapterOutputFilePath } \
${"--contamsOutputFile " + contamsOutputFilePath } \
--
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