From bbeef08f838dacf283cee14a5b1494e46f8fbbe8 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Jun 2020 15:39:32 +0200
Subject: [PATCH] make compression level optional for gather bam files
---
picard.wdl | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/picard.wdl b/picard.wdl
index 8962c4b..1d8376c 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -366,7 +366,7 @@ task GatherBamFiles {
Int memoryMb = javaXmxMb + 512
Int javaXmxMb = 1024
- Int compressionLevel = 1
+ Int? compressionLevel
Boolean createMd5File = false
# One minute per input gigabyte.
Int timeMinutes = 1 + ceil(size(inputBams, "G") * 1)
@@ -380,7 +380,7 @@ task GatherBamFiles {
GatherBamFiles \
INPUT=~{sep=' INPUT=' inputBams} \
OUTPUT=~{outputBamPath} \
- COMPRESSION_LEVEL=~{compressionLevel} \
+ ~{"COMPRESSION_LEVEL=" + compressionLevel} \
CREATE_INDEX=true \
CREATE_MD5_FILE=~{true="true" false="false" createMd5File}
}
--
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