From e1a70e6eb433d18ee5cd028d16551e3b7b4171b7 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 5 Apr 2018 15:18:16 +0200
Subject: [PATCH] rename gff to gtf
---
htseq.wdl | 4 ++--
stringtie.wdl | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/htseq.wdl b/htseq.wdl
index bccbdd2..6376e3e 100644
--- a/htseq.wdl
+++ b/htseq.wdl
@@ -1,7 +1,7 @@
task HTSeqCount {
String? preCommand
Array[File] alignmentFiles
- File gffFile
+ File gtfFile
String outputTable
String? format
String? order
@@ -17,7 +17,7 @@ task HTSeqCount {
-r ${default="pos" order} \
-s ${default="no" stranded} \
${sep=" " alignmentFiles} \
- ${gffFile} \
+ ${gtfFile} \
> ${outputTable}
}
diff --git a/stringtie.wdl b/stringtie.wdl
index 2f20133..a938b14 100644
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -1,7 +1,7 @@
task Stringtie {
String? preCommand
File alignedReads
- File? referenceGFF
+ File? referenceGtf
Int? threads
String assembledTranscriptsFile
Boolean? firstStranded
@@ -13,7 +13,7 @@ task Stringtie {
${preCommand}
stringtie \
${"-p " + threads} \
- ${"-G " + referenceGFF} \
+ ${"-G " + referenceGtf} \
${true="--rf" false="" firstStranded} \
${true="fr" false="" secondStranded} \
-o ${assembledTranscriptsFile} \
--
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