From c535d259e32ffb2ed409585c8d9bb1d2a61a0008 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 15 May 2020 10:23:58 +0200
Subject: [PATCH] fix variable used for time_minutes estimation in bwa
---
bwa.wdl | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/bwa.wdl b/bwa.wdl
index 01dae9b..3dd7883 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -29,7 +29,7 @@ task Mem {
String? readgroup
Int threads = 4
- String memory = "~{5 + ceil(size(indexFiles, "G"))}G"
+ String memory = "~{5 + ceil(size(bwaIndex.indexFiles, "G"))}G"
String picardXmx = "4G"
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 200 / threads)
# A mulled container is needed to have both picard and bwa in one container.
--
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