This requires that you specify the 'site name' as a flag to turn
on creating the srf files.Add the ability not to build srf files.
compress_eland_results(g, cycle_dir)
# build srf commands
compress_eland_results(g, cycle_dir)
# build srf commands
- lanes = range(1,9)
- run_name = srf.pathname_to_run_name(r.pathname)
- srf_cmds = srf.make_commands(run_name, lanes, site, cycle_dir)
- srf.run_srf_commands(r.bustard.pathname, srf_cmds, 2)
+ if site is not None:
+ lanes = range(1,9)
+ run_name = srf.pathname_to_run_name(r.pathname)
+ srf_cmds = srf.make_commands(run_name, lanes, site, cycle_dir)
+ srf.run_srf_commands(r.bustard.pathname, srf_cmds, 2)
def rm_list(files, dry_run=True):
for f in files:
def rm_list(files, dry_run=True):
for f in files:
parser.add_option('--run-xml', dest='run_xml',
default=None,
help='specify a run_<FlowCell>.xml file for summary reports')
parser.add_option('--run-xml', dest='run_xml',
default=None,
help='specify a run_<FlowCell>.xml file for summary reports')
- parser.add_option('--site', default='individual',
- help='specify the site name for srf files')
+ parser.add_option('--site', default=None,
+ help='create srf files tagged with the provided site name')
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 '
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 '