From b4fe827a3a02e2ec038d48781cf490771ad34d97 Mon Sep 17 00:00:00 2001
From: ffinfo <pjrvanthof@gmail.com>
Date: Wed, 12 Sep 2018 13:23:42 +0200
Subject: [PATCH] changed names
---
stringtie.wdl | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/stringtie.wdl b/stringtie.wdl
index b5346c3..b26109d 100644
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -5,7 +5,7 @@ import "common.wdl"
task Stringtie {
input {
String? preCommand
- IndexedBamFile bam
+ IndexedBamFile bamFile
File? referenceGtf
Int threads = 1
String assembledTranscriptsFile
@@ -25,7 +25,7 @@ task Stringtie {
~{true="fr" false="" secondStranded} \
-o ~{assembledTranscriptsFile} \
~{"-A " + geneAbundanceFile} \
- ~{bam.file}
+ ~{bamFile.file}
}
output {
--
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