From 6b71e72ca5a9b67f249575151ffd77d811572ae3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Fern=C3=A1ndez=20Navarro?=
 <jc.fernandez.navarro@gmail.com>
Date: Fri, 3 Sep 2021 10:30:54 +0200
Subject: [PATCH] Fix bug in gffread module

Update the output name in the command so it does no fail when the input has a .gtf extension.
---
 modules/gffread/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/gffread/main.nf b/modules/gffread/main.nf
index 6c5aecbc..7c024109 100644
--- a/modules/gffread/main.nf
+++ b/modules/gffread/main.nf
@@ -28,7 +28,7 @@ process GFFREAD {
     script:
     def software = getSoftwareName(task.process)
     """
-    gffread $gff $options.args -o ${gff.baseName}.gtf
+    gffread $gff $options.args -o ${gff.baseName}.out.gtf
     echo \$(gffread --version 2>&1) > ${software}.version.txt
     """
 }