From 3cb3a22426b02f1fb40062627e104cccb1d065b5 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 9 May 2018 13:14:16 +0200
Subject: [PATCH] fix bwamem task

---
 bwa.wdl | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/bwa.wdl b/bwa.wdl
index 2d9502e..e97ae48 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -1,4 +1,4 @@
-task BwaMem {
+task mem {
     String? preCommand
     File inputR1
     File? inputR2
@@ -10,6 +10,7 @@ task BwaMem {
     Int? threads
     Int? memory
 
+
     command {
         set -e -o pipefail
         mkdir -p $(dirname ${outputPath})
@@ -23,8 +24,8 @@ task BwaMem {
         File bamFile = outputPath
     }
     runtime{
-        cpu: if defined(threads) then threads else 1
-        memory: if defined(memory) then memory else 8
+        cpu: select_first([threads,1])
+        memory: select_first([memory,8])
     }
 }
 
-- 
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