From 8ed046481c7684963c55813fef795bd869858840 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 15 Jul 2019 14:32:12 +0200
Subject: [PATCH] add allow contain
---
bowtie.wdl | 2 ++
1 file changed, 2 insertions(+)
diff --git a/bowtie.wdl b/bowtie.wdl
index 046beea..0842581 100644
--- a/bowtie.wdl
+++ b/bowtie.wdl
@@ -33,6 +33,7 @@ task Bowtie {
Int? k
Boolean best = false
Boolean strata = false
+ Boolean allowContain = false
String? samRG
Int threads = 1
Int memory = 8
@@ -55,6 +56,7 @@ task Bowtie {
~{"-k " + k} \
~{true="--best" false="" best} \
~{true="--strata" false="" strata} \
+ ~{true="--allow-contain" false="" allowContain} \
~{"--threads " + threads} \
~{"--sam-RG '" + samRG}~{true="'" false="" defined(samRG)} \
~{sub(indexFiles[0], "(\.rev)?\.[0-9]\.ebwt$", "")} \
--
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