From 9d7eaa0ddd41a25386020371472395d44889d543 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 17 Jun 2019 08:41:21 +0200
Subject: [PATCH] add sam RG stuff
---
bowtie.wdl | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/bowtie.wdl b/bowtie.wdl
index 0876c82..f21bfef 100644
--- a/bowtie.wdl
+++ b/bowtie.wdl
@@ -34,6 +34,7 @@ task Bowtie {
Boolean best = false
Boolean strata = false
Boolean sam = true # Sane default
+ String? samRG
Int threads = 1
Int memory = 8
Int picardMemory = 4
@@ -51,6 +52,9 @@ task Bowtie {
~{"-k " + k} \
~{true="--best" false="" best} \
~{true="--strata" false="" strata} \
+ ~{"--threads " + threads} \
+ ~{true="--sam" false="" sam} \
+ ~{"--sam-RG " + samRG} \
-1 ~{sep="," readsUpstream} \
~{true="-2" false="" defined(readsDownstream)} ~{sep="," readsDownstream} \
| picard -Xmx~{picardMemory}G SortSam \
--
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