return path_fields[-1]
def _get_runfolder_name(self):
- if self.gerald is None:
- return None
- else:
+ if self.gerald:
return self.gerald.runfolder_name
+ elif hasattr(self.image_analysis, 'runfolder_name'):
+ return self.image_analysis.runfolder_name
+ else:
+ return None
runfolder_name = property(_get_runfolder_name)
def get_elements(self):
output_base_dir = os.getcwd()
for r in runs:
- result_dir = os.path.join(output_base_dir, r.flowcell_id)
- LOGGER.info("Using %s as result directory" % (result_dir,))
- if not os.path.exists(result_dir):
- os.mkdir(result_dir)
-
- # create cycle_dir
- cycle = "C%d-%d" % (r.image_analysis.start, r.image_analysis.stop)
- LOGGER.info("Filling in %s" % (cycle,))
- cycle_dir = os.path.join(result_dir, cycle)
- cycle_dir = os.path.abspath(cycle_dir)
- if os.path.exists(cycle_dir):
- LOGGER.error("%s already exists, not overwriting" % (cycle_dir,))
- continue
- else:
- os.mkdir(cycle_dir)
-
- # save run file
- r.save(cycle_dir)
-
- # save illumina flowcell status report
- save_flowcell_reports(os.path.join(r.image_analysis.pathname, '..'),
- cycle_dir)
-
- # save stuff from bustard
- # grab IVC plot
- save_ivc_plot(r.bustard, cycle_dir)
-
- # build base call saving commands
- if site is not None:
- save_raw_data(num_jobs, r, site, raw_format, cycle_dir)
-
- # save stuff from GERALD
- # copy stuff out of the main run
- g = r.gerald
-
- # save summary file
- save_summary_file(r, cycle_dir)
-
- # compress eland result files
- compress_eland_results(g, cycle_dir, num_jobs)
-
- # md5 all the compressed files once we're done
- md5_commands = srf.make_md5_commands(cycle_dir)
- srf.run_commands(cycle_dir, md5_commands, num_jobs)
+ result_dir = os.path.join(output_base_dir, r.flowcell_id)
+ LOGGER.info("Using %s as result directory" % (result_dir,))
+ if not os.path.exists(result_dir):
+ os.mkdir(result_dir)
+
+ # create cycle_dir
+ cycle = "C%d-%d" % (r.image_analysis.start, r.image_analysis.stop)
+ LOGGER.info("Filling in %s" % (cycle,))
+ cycle_dir = os.path.join(result_dir, cycle)
+ cycle_dir = os.path.abspath(cycle_dir)
+ if os.path.exists(cycle_dir):
+ LOGGER.error("%s already exists, not overwriting" % (cycle_dir,))
+ continue
+ else:
+ os.mkdir(cycle_dir)
+
+ # save run file
+ r.save(cycle_dir)
+
+ # save illumina flowcell status report
+ save_flowcell_reports(os.path.join(r.image_analysis.pathname, '..'),
+ cycle_dir)
+
+ # save stuff from bustard
+ # grab IVC plot
+ save_ivc_plot(r.bustard, cycle_dir)
+
+ # build base call saving commands
+ if site is not None:
+ save_raw_data(num_jobs, r, site, raw_format, cycle_dir)
+
+ # save stuff from GERALD
+ # copy stuff out of the main run
+ g = r.gerald
+
+ # save summary file
+ save_summary_file(r, cycle_dir)
+
+ # compress eland result files
+ compress_eland_results(g, cycle_dir, num_jobs)
+
+ # md5 all the compressed files once we're done
+ md5_commands = srf.make_md5_commands(cycle_dir)
+ srf.run_commands(cycle_dir, md5_commands, num_jobs)
def save_raw_data(num_jobs, r, site, raw_format, cycle_dir):
lanes = []
- for lane in range(1, 9):
+ for lane in r.gerald.lanes:
lane_parameters = r.gerald.lanes.get(lane, None)
- if lane_parameters is not None and lane_parameters.analysis != 'none':
+ if lane_parameters is not None:
lanes.append(lane)
run_name = srf.pathname_to_run_name(r.pathname)