From 355376870655f1c23477736a876f5f0268efb99f Mon Sep 17 00:00:00 2001
From: Katarzyna Sikora <sikora@pc329.immunbio.mpg.de>
Date: Mon, 17 Sep 2018 08:42:37 +0200
Subject: [PATCH] added mode alignment to RNAseq cmd

---
 app.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app.R b/app.R
index 3a59454..23f4988 100755
--- a/app.R
+++ b/app.R
@@ -185,7 +185,7 @@ server <- function(input, output, session) {
            
            else if(values$inWorkflow=="RNA-seq"){
              
-             values$command<-sprintf("mkdir -p %s ; %s ; %s ; %s -i %s -o %s --DE %s %s ",indir,link_cmd,cp_sInfo_cmd,path_to_exec,indir,outdir,values$sInfo_in,values$genome) 
+             values$command<-sprintf("mkdir -p %s ; %s ; %s ; %s --mode alignment -i %s -o %s --DE %s %s ",indir,link_cmd,cp_sInfo_cmd,path_to_exec,indir,outdir,values$sInfo_in,values$genome) 
              output$command<-renderText({ values$command })
              
            } #end of RNA-seq