Commit 475e2cd7 authored by Glenn Hickey's avatar Glenn Hickey
Browse files

pass through cores options in align-batch subjobs

parent c0cc1076
Pipeline #1543 failed with stage
in 7 minutes and 26 seconds
......@@ -873,7 +873,10 @@ def align_toil(job, chrom, seq_file_id, paf_file_id, config_id, options):
log_file = os.path.join(work_dir, '{}.hal.log'.format(chrom))
cmd = ['cactus-align', js, seq_file, paf_file, out_file, '--logFile', log_file, '--configFile', config_file] + options.alignOptions.split()
cores=options.alignCoresOverrides[chrom] if chrom in options.alignCoresOverrides else options.alignCores
if cores:
cmd += ['--consCores', str(cores)]
cmd += ['--maxCores', str(cores)]
ret_ids = [None, None, None, None]
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