def __init__(self): Job.__init__(self) self.input_bam = None self.reference_sequence = None self.output = None self.jobname = "svict-sv-calling"
def __init__(self):
Job.__init__(self)
self.input = None
self.output = None
self.jobname = "interval-list-to-bed"
def __init__(self):
Job.__init__(self)
self.input = None
self.output = None
self.jobname = "slop-interval-list"
def __init__(self):
Job.__init__(self)
self.input = None
self.output = None
self.jobname = "filter-gtf-chrs"
def __init__(self):
Job.__init__(self)
self.input_contest_results = None
self.output = None
self.jobname = "contest_to_contam_qc"
def __init__(self):
Job.__init__(self)
self.output_dir = None
self.jobname = "fetch-vep-cache"
def __init__(self):
Job.__init__(self)
self.input_bam = None
self.input_bed = None
self.tag = None
self.output = None
def __init__(self, input_segments, output_bed, genes_gtf):
Job.__init__(self)
self.input_segments = input_segments
self.output_bed = output_bed
self.genes_gtf = genes_gtf
def __init__(self, input_bam, output_segments, background=None):
Job.__init__(self)
self.input = input_bam
self.output = output_segments
self.background = background
self.jobname = "qdnaseq"
def __init__(self):
Job.__init__(self)
self.input_bam = None
self.reference_genome = None
self.threads = None
self.output_bam = None
def __init__(self):
Job.__init__(self)
self.input_bam = None
self.output_bam = None
self.output_histogram = None
def __init__(self):
Job.__init__(self)
self.input_bam = None
self.output_bam = None
self.metrics_txt = None
self.reference_genome = None
def __init__(self):
Job.__init__(self)
self.input_msi_sites = None
self.target_bed = None
self.output_msi_sites = True
self.jobname = "msi-intersect"
def __init__(self):
Job.__init__(self)
self.input_fasta = None
self.output = None
self.homopolymers_only = True
self.jobname = "msisensor-scan"
def __init__(self):
Job.__init__(self)
self.input_vcf_hc = None
self.input_vcf_strelka = None
self.output_vcf = None
self.reference_genome = None
def __init__(self, input_file, output_file):
Job.__init__(self)
self.input = input_file
self.output = output_file
self.jobname = "copy"
def __init__(self):
Job.__init__(self)
self.input_vcf = None
self.oncokb_db = None
self.output = None
self.vcftype = None
def __init__(self):
Job.__init__(self)
self.input = None
self.output = None
self.jobname = "gunzip"
def __init__(self):
Job.__init__(self)
self.input_bam = None
self.input_bed = None
self.min_basequal = None
self.output = None
def __init__(self):
Job.__init__(self)
self.remote = None
self.output = None
self.jobname = "curl"
def __init__(self):
Job.__init__(self)
self.input = None
self.filter = None
self.output = None
self.jobname = "vcffilter"
def __init__(self):
Job.__init__(self)
self.input = None
self.output = None
self.jobname = "gtf2genepred"