From f0b59be2b37d8fecb2fcb00446e7caffa014868e Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 19 Jul 2019 13:13:46 +0200
Subject: [PATCH] use output compression level 1 for cutadapt
---
cutadapt.wdl | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/cutadapt.wdl b/cutadapt.wdl
index 6161d8b..56ac2c4 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -60,10 +60,11 @@ task Cutadapt {
Boolean? zeroCap
Boolean? noZeroCap
String? reportPath
+ Int compressionLevel = 1 # This only affects outputs with the .gz suffix.
Int cores = 1
Int memory = 16 # FIXME: Insane memory. Double-check if needed.
- String dockerImage = "quay.io/biocontainers/cutadapt:2.3--py36h14c3975_0"
+ String dockerImage = "quay.io/biocontainers/cutadapt:2.4--py37h14c3975_0"
}
String read2outputArg = if (defined(read2output))
@@ -95,6 +96,7 @@ task Cutadapt {
~{read2outputArg}
cutadapt \
~{"--cores=" + cores} \
+ ~{"--compression-level " + compressionLevel} \
~{true="-a" false="" defined(adapterForward)} ~{sep=" -a " adapterForward} \
~{true="-A" false="" defined(adapterReverse)} ~{sep=" -A " adapterReverse} \
~{true="-g" false="" defined(front)} ~{sep=" -g " front} \
--
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