From f8555ebe6e597d14e7c46febc81bdb284ae76c1c Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 22 Feb 2018 13:26:41 +0100
Subject: [PATCH] solved memory issues
---
bwa.wdl | 2 +-
cutadapt.wdl | 4 ++--
spades.wdl | 2 +-
3 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index fb222ad..a95bb25 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -6,7 +6,7 @@ task mem {
String? outputFile = "aligned.bam"
String? preCommand
Int? threads = 1
- String? memory = "4G"
+ Int? memory = 4
Int? minimumSeedLength
Int? w
Int? d
diff --git a/cutadapt.wdl b/cutadapt.wdl
index 4eb8b1b..6e6cd56 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -6,7 +6,7 @@ task cutadapt {
String? format
String? preCommand
Int? cores = 1
- String? memory = "4G"
+ Int? memory = 4
Array[String]+? adapter
Array[String]+? front
Array[String]+? anywhere
@@ -122,4 +122,4 @@ task cutadapt {
cpu: select_first([cores])
memory: select_first([memory])
}
-}
\ No newline at end of file
+}
diff --git a/spades.wdl b/spades.wdl
index 8c97c63..5a8ab28 100644
--- a/spades.wdl
+++ b/spades.wdl
@@ -74,6 +74,6 @@ task spades {
}
runtime {
cpu: select_first([threads])
- memory: select_first([memoryGb]) + "G"
+ memory: select_first([memoryGb])
}
}
\ No newline at end of file
--
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