from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines.runfolder import ElementTree
+LOGGER = logging.getLogger(__name__)
def main(cmdlist=None):
parser = make_parser()
opts, args = parser.parse_args(cmdlist)
logging.basicConfig()
- if opts.verbose:
- root_log = logging.getLogger()
+ root_log = logging.getLogger()
+ if opts.debug:
+ root_log.setLevel(logging.DEBUG)
+ elif opts.verbose:
root_log.setLevel(logging.INFO)
logging.info('Starting htsworkflow illumina runfolder processing tool.')
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('-v', '--verbose', dest='verbose', action='store_true',
default=False,
help='turn on verbose mode')
+ parser.add_option('--debug', action='store_true',
+ default=False,
+ help='turn on debug logging (implies verbose)')
parser.add_option('--dry-run', action='store_true', default=False,
help="Don't delete anything (in clean mode)")
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'],
+ 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')
+ 'Currently supported options: qseq, srf, fastq')
parser.add_option('-u', '--use-run', dest='use_run', default=None,
help='Specify which run to use instead of autoscanning '
'the runfolder. You do this by providing the final '