task.py put arg_cmd back in the mixcr command

server/web2py/applications/vidjil/models/task.py

@@ -234,7 +234,7 @@ def run_mixcr(id_file, id_config, id_data, id_fuse, clean_before=False, clean_af
     mixcr = defs.DIR_MIXCR + 'mixcr'
     cmd = mixcr + ' align --save-reads -t 1 -r ' + report + '.aln'
     #+ output_filename
-    cmd += ' ' + seq_file  + ' ' + out_alignments
+    cmd += ' ' + arg_cmd + ' ' + seq_file  + ' ' + out_alignments
     cmd += ' && ' + mixcr + ' assemble -t 1 -r ' + report + '.asmbl ' + out_alignments + ' ' + out_clones
     cmd += ' && ' + mixcr + ' exportClones -t 1 --format vidjil -germline -id -name -reads -sequence -top -seg -s ' + out_clones + ' ' + out_results