From 366f8ef151c4f05a958f94836cb0f789e32715ef Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 16 Mar 2018 15:26:30 +0100
Subject: [PATCH] add abundance file option to stringtie
---
stringtie.wdl | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/stringtie.wdl b/stringtie.wdl
index d569481..e969ac7 100644
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -6,6 +6,7 @@ task Stringtie {
String assembledTranscriptsFile
Boolean? firstStranded
Boolean? secondStranded
+ String? geneAbundanceFile
command {
set -e -o pipefail
@@ -15,12 +16,15 @@ task Stringtie {
${"-G " + referenceGFF} \
${true="--rf" false="" firstStranded} \
${true="fr" false="" secondStranded} \
+ -o ${assembledTranscriptsFile} \
+ ${"-A " + geneAbundanceFile} \
${alignedReads} \
- > ${assembledTranscriptsFile}
+
}
output {
File assembledTranscripts = assembledTranscriptsFile
+ File geneAbundance = geneAbundanceFile
}
runtime {
--
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