# HG changeset patch
# User p.lucas
# Date 1723102842 0
# Node ID 8e5694208b798ea46a67f62d629eb50b69aedaa4
# Parent  f8e542216aea8f831fc9c1c6555f90d73e2267ca
Uploaded

diff -r f8e542216aea -r 8e5694208b79 Prepare_Ssuis_serotypingPipeline.py
--- a/Prepare_Ssuis_serotypingPipeline.py	Thu Aug 08 07:30:38 2024 +0000
+++ b/Prepare_Ssuis_serotypingPipeline.py	Thu Aug 08 07:40:42 2024 +0000
@@ -57,12 +57,16 @@
   input_path = os.path.splitext(output2)[0]+"_input_file_test/"
   output_path = os.path.splitext(output2)[0]+"_Results/"
   os.system("mkdir -p "+input_path)
-  os.system("cp "+ffile+" "+input_path+"/file_test.fastq") 
   fdir = input_path
 
   if ends == "se":
     f = "SINGLE"
     r = "SINGLE"
+    os.system("cp "+ffile+" "+input_path+"/file_test.fastq")
+
+  elif ends == "pe":
+    os.system("cp "+ffile+" "+input_path+"/file_test"+f+".fastq")
+    os.system("cp "+ffile+" "+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))