Commit 2a078d1c authored by HERBERT Ryan's avatar HERBERT Ryan

task.py switching mixcr to single-threadedw

parent 9b8778f9
......@@ -232,12 +232,11 @@ def run_mixcr(id_file, id_config, id_data, id_fuse, clean_before=False, clean_af
## commande complete
mixcr = defs.DIR_MIXCR + 'mixcr'
cmd = mixcr + ' align --save-reads -t 3 -r ' + report + '.aln'
cmd = mixcr + ' align --save-reads -t 1 -r ' + report + '.aln'
#+ output_filename
# TODO reduce threads
cmd += ' ' + seq_file + ' ' + out_alignments
cmd += ' && ' + mixcr + ' assemble -t 3 -r ' + report + '.asmbl ' + out_alignments + ' ' + out_clones
cmd += ' && ' + mixcr + ' exportClones -t 3 --format vidjil -germline -id -name -reads -sequence -top -seg -s ' + out_clones + ' ' + out_results
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
## execute la commande MiXCR
print "=== Launching MiXCR ==="
......
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