runs = []
if opts.run_xml:
# handle ~ shortcut
- opt.run_xml = os.path.expanduser(opt.run_xml)
- tree = ElementTree.parse(opt.run_xml).getroot()
+ opts.run_xml = os.path.expanduser(opts.run_xml)
+ tree = ElementTree.parse(opts.run_xml).getroot()
runs.append(runfolder.PipelineRun(xml=tree))
return runs
parser.add_option('--site', default=None,
help='create srf files tagged with the provided '\
'site name')
- parser.add_option('--raw-format', dest="raw_format", default='qseq',
- choices=['qseq', 'srf', 'fastq'],
+ parser.add_option('--raw-format', dest="raw_format", default=None,
+ choices=['qseq', 'srf', 'fastq', None],
help='Specify which type of raw format to use. '
'Currently supported options: qseq, srf, fastq')
parser.add_option('-u', '--use-run', dest='use_run', default=None,