def __init__(self,config,key=int(-1),input_dir=None,fastq_archive=None,flowcell=None,machine=None,date='dummy',run_number='dummy',side='dummy',operator=None,run_type=None,process_name='sequencing_run',no_delete=False,sample_sheet=None,**kwargs):
"""
Initializes the object.
"""
if not input_dir is None:
GenericProcess.__init__(self,config,key=key,**kwargs)
self.input_dir = input_dir
self.flowcell_key = flowcell.key
self.machine_key = machine.key
self.date = date
self.run_number = run_number
self.side = side
self.state = "Running"
self.operator = operator
self.run_type = run_type
self.bcltofastq_pipeline_key = None
#self.input_amount = input_amount
#self.yield_from_library = yield_from_library
#self.average_bp = average_bp
output_name_pieces = []
output_name_pieces.append(str(date))
output_name_pieces.append(str(machine.key))
output_name_pieces.append(str(run_number))
output_name_pieces.append(str(side)+str(flowcell.key))
output_name = "_".join(output_name_pieces)
self.output_dir = os.path.join(config.get('Common_directories','hiseq_output'),output_name)
if fastq_archive is None:
self.fastq_archive = os.path.join(config.get('Common_directories','casava_output'),output_name)
else:
self.fastq_archive = fastq_archive
self.complete_file = os.path.join(config.get('Common_directories','hiseq_output'),output_name+"/"+config.get('Filenames','bcls_ready'))
self.no_delete = no_delete
self.interop_archived = False
self.sample_sheet = sample_sheet
def __init__(self,config,key=int(-1),flowcell=None,seq_run=None,base_output_dir=None,process_name='flowcell_reports',**kwargs):
"""
Initiates the report object attached to the flowcell and sequencing run
but not attached to any pipelines as of yet.
"""
if not flowcell is None:
GenericProcess.__init__(self,config,key=key,process_name=process_name,**kwargs)
if base_output_dir == None:
self.base_output_dir = config.get('Common_directories','flowcell_reports')
else:
self.base_output_dir = base_output_dir
self.flowcell_key = flowcell.key
self.sequencing_run_key = seq_run.key
self.sequencing_run_type = seq_run.run_type
self.pipelines = None
numbers = config.get('Flowcell_reports','numbers').split(',')
for number in numbers:
setattr(self,'flowcell_report_' + str(number) + '_key',None)
self.state = 'Running'
