def __init__(self, primer3_dir="", trf_dir="", primer3_bin="primer3_core", trf_bin="trf",
glistmaker_dir="", glistmaker_bin="glistmaker", primer3_thermo_config_dir=None):
Pipeline.__init__(self)
self.primer3_dir = primer3_dir
self.trf_dir = trf_dir
self.primer3_bin = primer3_bin
self.trf_bin = trf_bin
self.glistmaker_dir = glistmaker_dir
self.glistmaker_bin = glistmaker_bin
self.primer3_thermo_config_dir = primer3_thermo_config_dir
def __init__(self,
max_threads=1,
max_memory=10,
GATK_dir="",
GATK_jar="GenomeAnalysisTK.jar",
Picard_dir=""):
Pipeline.__init__(self, max_threads=max_threads, max_memory=max_memory)
self.GATK_dir = GATK_dir
self.GATK_jar = GATK_jar
self.Picard_dir = Picard_dir
def __init__(self,
max_threads=1,
max_memory=10,
BWA_dir="",
BWA_binary=None,
bowtie2_dir="",
bowtie2_binary=None,
Picard_dir=""):
Pipeline.__init__(self, max_threads=max_threads, max_memory=max_memory)
self.BWA_dir = BWA_dir
self.bowtie2_dir = bowtie2_dir
self.Picard_dir = Picard_dir
self.BWA_binary = BWA_binary
self.bowtie2_binary = bowtie2_binary
def __init__(self, workdir="./", max_threads=1):
Pipeline.__init__(self, workdir=workdir, max_threads=max_threads)
self.dirs = {
"fastq": {
"raw": [],
"trimmed": [],
},
"fasta": {
"raw": [],
"trimmed": [],
},
"qual_plot": {
"raw": [],
"trimmed": [],
},
}
self.sanger_extention_list = [".ab1"]
def __init__(self):
Pipeline.__init__(self)