def __init__(self,config,key=int(-1),process_name='merge_bam',prev_step=None,**kwargs):
"""
Initializes the process object.
"""
if not prev_step is None:
Bam2BamQsubProcess.__init__(self,config,key=key,process_name=process_name,input_dir=prev_step.output_dir,output_dir=prev_step.output_dir,prev_step=prev_step,**kwargs)
self.output_bam = os.path.join(self.output_dir,self.sample_key + ".sort.bam");#Overwrites because only a single file is needed.
def __init__(self,config,key=int(-1),process_name='mark_duplicates',prev_step=None,**kwargs):
"""
Initializes the process object.
"""
if not prev_step is None:
Bam2BamQsubProcess.__init__(self,config,key=key,new_bam_description="dedup",process_name=process_name,input_dir=prev_step.output_dir,output_dir=prev_step.output_dir,prev_step=prev_step,**kwargs)
qc_dir = re.sub(r"align$","qc",self.output_dir)
if not os.path.isdir(qc_dir) and not re.search('dummy',self.output_dir):
os.makedirs(qc_dir)
self.output_metrics = os.path.join(qc_dir,self.sample_key + ".dedup_metrics");
def __init__(self,config,key=int(-1),process_name='indel_realignment',pipeline_config=None,prev_step=None,**kwargs):
"""
Initializes the process object.
"""
if not prev_step is None:
Bam2BamQsubProcess.__init__(self,config,key=key,new_bam_description="realign",process_name=process_name,input_dir=prev_step.output_dir,output_dir=prev_step.output_dir,prev_step=prev_step,**kwargs)
self.output_intervals = os.path.join(self.output_dir,self.sample_key + ".intervals");
self.ref_fa = pipeline_config.get('References','genome_fasta')
known_databases = []
known_databases.append(pipeline_config.get('References','gold_indels_vcf'))
known_databases.append(pipeline_config.get('References','one_k_indels_vcf'))
self.known_database = ":".join(known_databases)
def __init__(self,config,key=int(-1),process_name='sort_bam',prev_step=None,**kwargs):
"""
Initializes the process object.
"""
if not prev_step is None:
Bam2BamQsubProcess.__init__(self,config,key=key,new_bam_description="sort",process_name=process_name,input_dir=prev_step.output_dir,output_dir=prev_step.output_dir,number_tasks=prev_step.number_tasks,prev_step=prev_step,**kwargs)