From e4fdd5ba9d4457ef56fc331df9acad754cb42530 Mon Sep 17 00:00:00 2001
From: aceol <arnaud.ceol.pro@gmail.com>
Date: Wed, 13 Jul 2016 14:19:32 +0200
Subject: [PATCH] fix wrong variable name with RNAseq causing removing twice
 the output

---
 pipeline/merging.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pipeline/merging.R b/pipeline/merging.R
index 40b1dc8..7651eab 100755
--- a/pipeline/merging.R
+++ b/pipeline/merging.R
@@ -184,7 +184,7 @@ merging <- function ( flags, flagsPRE, id_merge_primary ) {
 		updateInfoOnDB( SQL )
 		
 		if ( paired ) {
-			cmd <- paste(
+			execute <- paste(
 					getHTSFlowPath("featuresCounts")
 					,"-T 16 -p -P -a"
 					,gtf
@@ -195,7 +195,7 @@ merging <- function ( flags, flagsPRE, id_merge_primary ) {
 			)
 			tryOrExit(execute, "feature counts")
 		} else {
-			cmd <- paste(
+			execute <- paste(
 					getHTSFlowPath("featuresCounts")
 					,"-T 16 -a"
 					,gtf