From e5a86409f606da5756dd00f2c798bd41aee5c1a5 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 16 Mar 2018 14:45:38 +0100
Subject: [PATCH] add strandedness to stringtie
---
stringtie.wdl | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/stringtie.wdl b/stringtie.wdl
index cba7076..d569481 100644
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -4,6 +4,8 @@ task Stringtie {
File? referenceGFF
Int? threads
String assembledTranscriptsFile
+ Boolean? firstStranded
+ Boolean? secondStranded
command {
set -e -o pipefail
@@ -11,6 +13,8 @@ task Stringtie {
stringtie \
${"-p " + threads} \
${"-G " + referenceGFF} \
+ ${true="--rf" false="" firstStranded} \
+ ${true="fr" false="" secondStranded} \
${alignedReads} \
> ${assembledTranscriptsFile}
}
--
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