# HG changeset patch
# User p.lucas
# Date 1723104081 0
# Node ID 07cf23fc69c8244c0177b588991db78664ed1c71
# Parent  76c82b2a43d23957b85fb5911b9f5719d26c9914
Uploaded

diff -r 76c82b2a43d2 -r 07cf23fc69c8 Prepare_Ssuis_serotypingPipeline.py
--- a/Prepare_Ssuis_serotypingPipeline.py	Thu Aug 08 08:01:10 2024 +0000
+++ b/Prepare_Ssuis_serotypingPipeline.py	Thu Aug 08 08:01:21 2024 +0000
@@ -3,14 +3,12 @@
 #Libraries:
 import os, os.path, argparse, sys, gzip, re
 
-
-
 ##### MAIN
 def __main__():
   ### Arguments:
   parser = argparse.ArgumentParser(description='''Launch Ssuis_serotypingPipeline.pl with correct argument''', epilog="""This script needs few options use -h to see it.""")
-
   parser.add_argument('--fastq_file', dest='ffile')
+  parser.add_argument('--fastq_file2', dest='ffile2')
   parser.add_argument('--scoreName', dest='sname')
   parser.add_argument('--output2', dest='o2')
   parser.add_argument('--output3', dest='o3')
@@ -33,6 +31,7 @@
   ### Get argument in variable:
   options = parser.parse_args()
   ffile = options.ffile
+  ffile2 = options.ffile2
   sname = options.sname
   output2 = options.o2
   output3 = options.o3
@@ -66,7 +65,7 @@
 
   elif ends == "pe":
     os.system("cp "+ffile+" "+input_path+"/file_test"+f+".fastq")
-    os.system("cp "+ffile+" "+input_path+"/file_test"+r+".fastq")
+    os.system("cp "+ffile2+" "+input_path+"/file_test"+r+".fastq")
 
   if sd is None:
     os.system("perl "+way_pipeline+"/Ssuis_serotypingPipeline.pl --fastq_directory "+str(fdir)+" --scoreName "+output_path+"Results --ends "+str(ends)+" --forward "+str(f)+" --reverse "+str(r))