Commit 403773ad authored by HERBERT Ryan's avatar HERBERT Ryan

task.py put arg_cmd back in the mixcr command

parent ca491ad7
......@@ -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
......
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