Commit 4ac9f97f authored by Mathieu Giraud's avatar Mathieu Giraud Committed by Vidjil Team

task.py: do not use -G option if 'multi' germline is selected

parent 41cadbc8
......@@ -82,7 +82,10 @@ def run_vidjil(id_file, id_config, id_data, id_fuse):
vidjil_germline = db.config[id_config].germline
## commande complete
cmd = vidjil_path+'/vidjil ' + ' -o ' + out_folder + ' -G ' + germline_folder + vidjil_germline + ' '+ vidjil_cmd+' '+ seq_file
cmd = vidjil_path+'/vidjil ' + ' -o ' + out_folder
if not vidjil_germline == 'multi':
cmd += ' -G ' + germline_folder + vidjil_germline
cmd += ' ' + vidjil_cmd + ' '+ seq_file
## execute la commande vidjil
p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT, close_fds=True)
......
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