def load_configuration(self):
config = pipeline_config.Config()
conf_dict = config.get_config_dict([
NOTIFY_EMAIL, CORES, GENOME, BCBIO_BACKUP, MUTREPORT_CANCERGENES,
MUTREPORT_CGC
])
return conf_dict
def load_configuration(self):
config = pipeline_config.Config()
conf_dict = config.get_config_dict([NOTIFY_EMAIL,
CORES,
GENOME,
BCBIO_BACKUP])
return conf_dict
def load_configuration(self):
config = pipeline_config.Config()
conf_dict = config.get_config_dict([
NOTIFY_EMAIL, CORES, GENOME, SAMTOOLS_BIN, BCFTOOLS_BIN,
SAMBAMBA_BIN
])
return conf_dict
def load_configuration(self):
config = pipeline_config.Config()
conf_dict = config.get_config_dict([
NOTIFY_EMAIL, CORES, GENOME, TRANSCRIPT_GTF, TRANSCRIPT_GTF_MASK,
CUFFLINKS_BIN
])
return conf_dict
def load_configuration(self):
config = pipeline_config.Config()
conf_dict = config.get_config_dict([
STAR_CORES, STAR_GENOME_DIR, NOTIFY_EMAIL, STAR_BIN, CUTADAPT_BIN,
CUTADAPT_ADAPTERS, SAMBAMBA_BIN, CORES
])
conf_dict[STAR_OVERHANG] = self.read_sjdboverhang(conf_dict)
return conf_dict
def load_configuration(self):
config = pipeline_config.Config()
conf_dict = config.get_config_dict([NOTIFY_EMAIL,
GENOME,
BCBIO_BACKUP,
POPVAR_EXACSNP_BED,
POPVAR_COSMIC_BED,
MUTREPORT_CGC])
return conf_dict
def load_configuration(self):
config = pipeline_config.Config()
conf_dict = config.get_config_dict([NOTIFY_EMAIL])
return conf_dict
def load_configuration(self):
config = pipeline_config.Config()
conf_dict = config.get_config_dict(
[RNASEQC_JAR, TRANSCRIPT_GTF, NOTIFY_EMAIL, GENOME])
return conf_dict
def __init__(self, patient_dir, patientid=None):
self.conf_dict = pipeline_config.Config().get_config_dict(
[BCBIO_BACKUP, NOTIFY_EMAIL])
self.patient_dir = patient_dir
self.patient = self.derive_patient_name(patient_dir, patientid)
def load_configuration(self):
config = pipeline_config.Config()
conf_dict = config.get_config_dict([
QUALIMAP_BIN, TRANSCRIPT_GTF, TARGET_REGIONS, NOTIFY_EMAIL, CORES
])
return conf_dict
def load_configuration(self):
config = pipeline_config.Config()
conf_dict = config.get_config_dict(
[NOTIFY_EMAIL, DEFUSE_CORES, DEFUSE_DATA_DIR, DEFUSE_CONFIG])
return conf_dict