def process(self):
# Reduce inputs to only first element
if hasattr(self.input_dir, '__iter__'):
self.input_dir = self.input_dir[0]
if not self.input_dir.endswith('/'):
self.input_dir += '/'
(parent_dir, flowcell_dir) = os.path.split(os.path.dirname(self.input_dir))
parsed = re.search(r'''(?P<DATE>\d{6})_
(?P<HISEQ_SN>\w{6})_
(?P<RUN_COUNT>\d{4})_
(?P<FC_POS>[AB])
(?P<FC_ID>.*$)''', flowcell_dir, re.X)
ss = SampleSheet(os.path.join(self.input_dir, 'SampleSheet.csv'))
ss_validated = os.path.join(self.output_dir, 'sample_sheet_validated.csv')
project_name = ss.get_project_name() or 'DefaultProject'
run_desc = 'Flowcell %s on %s/%s' % (parsed.group('FC_ID'),
os.path.basename(parent_dir),
parsed.group('FC_POS'))
self.meta.update({
'pipeline': {
'date' : parsed.group('DATE'),
'descr' : run_desc,
'fc_id' : parsed.group('FC_ID'),
'fc_pos' : parsed.group('FC_POS'),
'hiseq' : os.path.basename(parent_dir),
'hiseq_sn' : parsed.group('HISEQ_SN'),
'project_name' : project_name,
'run_count' : int(parsed.group('RUN_COUNT')),
'nfiles' : ss.get_lines_count()
}
})
ss_validated = ss.validate(project_name, ss_validated)
self.output_files = [ss_validated]
