def __init__(self):
Job.__init__(self)
self.input = None
self.output = None
self.outdir = None
self.extract = False
self.jobname = "fastqc"
def __init__(self):
Job.__init__(self)
self.msi_sites = None
self.input_normal_bam = None
self.input_tumor_bam = None
self.output = None
self.jobname = "msisensor"
def __init__(self):
Job.__init__(self)
self.input_cns = None
self.input_cnr = None
self.output_profile_bedgraph = None
self.output_segments_bedgraph = None
self.jobname = "make_cnvkit_tracks"
def __init__(self):
Job.__init__(self)
self.input = None
self.targets_bed = None
self.coverage_thresholds = [30, 50, 70, 100, 200, 300]
self.output = None
self.jobname = "sambamba-depth"
def __init__(self):
Job.__init__(self)
self.input_target_regions_bed_1 = None
self.input_target_regions_bed_2 = None
self.input_population_vcf = None
self.output = None
self.jobname = "create_contest_vcfs"
def __init__(self):
Job.__init__(self)
self.input_qdnaseq_file = None
self.output_segments_bedgraph = None
self.output_copynumber_tdf = None
self.output_readcount_tdf = None
self.jobname = "make_qdnaseq_tracks"
def __init__(self):
Job.__init__(self)
self.input_tumor_cnr = None
self.input_tumor_cns = None
self.input_normal_cnr = None
self.input_normal_cns = None
self.input_het_snps_vcf = None
self.input_purecn_csv = None
self.input_purecn_genes_csv = None
self.input_purecn_loh_csv = None
self.input_purecn_variants_csv = None
self.input_svcaller_T_DEL = None
self.input_svcaller_T_DUP = None
self.input_svcaller_T_INV = None
self.input_svcaller_T_TRA = None
self.input_svcaller_N_DEL = None
self.input_svcaller_N_DUP = None
self.input_svcaller_N_INV = None
self.input_svcaller_N_TRA = None
self.input_germline_mut_vcf = None
self.input_somatic_mut_vcf = None
self.output_plot_png = None
self.output_cna_json = None
self.output_purity_json = None
self.jobname = "liqbio-cna"
def __init__(self,
input_tumor=None,
input_normal=None,
tumorid=None,
normalid=None,
reference_sequence=None,
target_bed=None,
normal_pileup=None,
tumor_pileup=None,
output_snv=None,
output_indel=None,
output_somatic_snv=None,
output_somatic_indel=None):
Job.__init__(self)
self.input_tumor = input_tumor
self.input_normal = input_normal
self.tumorid = tumorid
self.normalid = normalid
self.reference_sequence = reference_sequence
self.target_bed = target_bed
self.normal_pileup = normal_pileup
self.tumor_pileup = tumor_pileup
self.output_indel = output_indel
self.output_snv = output_snv
self.output_somatic_snv = output_somatic_snv
self.output_somatic_indel = output_somatic_indel
def __init__(self):
Job.__init__(self)
self.input_fastq1 = None
self.input_fastq2 = None
self.output_bam = None
self.sample = None
self.library = None
def __init__(self,
input_seg=None,
input_vcf=None,
tumorid=None,
outdir=None,
gcgene_file=None,
minpurity=0.05,
hzdev=0.1,
seg_sdev=None,
genome="hg19",
postopt=False):
Job.__init__(self)
self.input_seg = input_seg
self.input_vcf = input_vcf
self.tumorid = tumorid # should be the same as the ID in the seg file
self.outdir = outdir
self.gcgene_file = gcgene_file
self.minpurity = minpurity
self.hzdev = hzdev
self.seg_sdev = seg_sdev
self.genome = genome
self.postopt = postopt
# FIXME: For PureCN jobs, the parameters *must* be specified to the constructor. This is inconsistent
# across different Job sub-classes.
# Determining output here purely as a means of determining when the job has
# completed; PureCN itself determines the output file paths based on the
# specified "--out" and "--sampleid" arguments.
self.output = "{}/{}_genes.csv".format(self.outdir, self.tumorid)
self.jobname = "purecn"
def __init__(self):
Job.__init__(self)
self.remote = None
self.input_reference_sequence = None
self.input_reference_sequence_fai = None
self.output = None
self.jobname = "curl-split-leftaln"
def __init__(self):
Job.__init__(self)
self.input_histogram = None
self.output = None
self.high_thresh_fraction = 0.95
self.high_thresh_fold_cov = 100
self.low_thresh_fraction = 0.95
self.low_thresh_fold_cov = 50
def __init__(self):
Job.__init__(self)
self.reference_genome = None
self.input_eval_bam = None
self.input_genotype_bam = None
self.input_population_af_vcf = None
self.output = None
self.jobname = "contest"
def __init__(self):
Job.__init__(self)
self.input_files = None
self.search_dir = None
self.output = None
self.report_title = None
self.data_format = 'json'
self.jobname = "multiqc"
def __init__(self):
Job.__init__(self)
self.input_vcf = None
self.output_vcf = None
self.reference_sequence = None
self.vep_dir = None
self.jobname = "vep"
self.additional_options = ""
def __init__(self):
Job.__init__(self)
self.input_vcf = None
self.input_bam = None
self.samplename = None
self.filter_hom = True
self.output = None
self.jobname = "vcf-add-sample"
def __init__(self, referral_db_conf, blood_barcode, tumor_barcode,
output_json, addresses):
Job.__init__(self)
self.referral_db_conf = referral_db_conf
self.blood_barcode = blood_barcode
self.tumor_barcode = tumor_barcode
self.output_json = output_json
self.addresses = addresses
def __init__(self):
Job.__init__(self)
self.input = None
self.reference_sequence = None
self.output_metrics = None
self.output_summary = None
self.stop_after = None
self.jobname = "picard-gcbias"
def __init__(self):
Job.__init__(self)
self.input_bam = None
self.reference_sequence = None
self.dbSNP = None
self.interval_list = None
self.java_options = "--java-options -Xmx10g"
self.output = None
self.jobname = "gatk-haplotype-germline"
def __init__(self):
Job.__init__(self)
self.input = None
self.reference_sequence = None
self.minimum_mapping_quality = None
self.minimum_base_quality = None
self.coverage_cap = None
self.output_metrics = None
self.jobname = "picard-wgsmetrics"
def __init__(self): Job.__init__(self) self.input_normal = None self.input_tumor = None self.target_bed = None self.output_sample = None self.reference_sequence = None self.threads = None self.jobname = "svaba-sv-calling"
def __init__(self):
Job.__init__(self)
self.input_bam = None
self.event_type = None
self.output_bam = None
self.output_gtf = None
self.reference_sequence = None
self.scratch = None
self.jobname = "svcaller-run-all"
def __init__(self):
Job.__init__(self)
self.input_vcf = None
self.input_bam = None
self.reference_sequence = None
self.target_regions = None
self.normalid = None
self.filter_reads_with_N_cigar = True
self.output = None
self.jobname = "hzconcordance"
def __init__(self):
Job.__init__(self)
self.input = None
self.reference_sequence = None
self.target_regions = None
self.bait_regions = None
self.bait_name = None
self.output_metrics = None
self.accumulation_level = ['LIBRARY']
self.jobname = "picard-hsmetrics"
def __init__(self,
input_genomic_json,
input_metadata_json,
output_pdf,
alascca_only=False):
Job.__init__(self)
self.input_metadata_json = input_metadata_json
self.input_genomic_json = input_genomic_json
self.output_pdf = output_pdf
self.alascca_only = alascca_only
def __init__(self):
Job.__init__(self)
self.input_tumor = None
self.input_normal = None
self.tumorid = None
self.normalid = None
self.reference_sequence = None
self.target_bed = None
self.output_dir = None
self.jobname = "manta-somatic-sv"
def __init__(self):
Job.__init__(self)
self.input_cnr = None
self.input_cns = None
self.input_germline_vcf = None
self.input_somatic_vcf = None
self.chrsizes = None
self.output_png = None
self.output_cna = None
self.output_purity = None
self.jobname = "alascca-cna"
def __init__(self,
input_bam,
output_bam,
output_metrics,
remove_duplicates=False):
Job.__init__(self)
self.input_bam = input_bam
self.output_bam = output_bam
self.output_metrics = output_metrics
self.remove_duplicates = remove_duplicates
self.jobname = "picard-markdups"
def __init__(self,
input_bams,
output_bam,
assume_sorted=True,
merge_dicts=True):
Job.__init__(self)
self.input_bams = input_bams
self.output_bam = output_bam
self.assume_sorted = assume_sorted
self.merge_dicts = merge_dicts
self.jobname = "picard-mergesamfiles"
def __init__(self): Job.__init__(self) self.input_normal = None self.input_tumor = None self.normal_discordants = None self.tumor_discordants = None self.normal_splitters = None self.tumor_splitters = None self.output = None self.threads = None self.jobname = "lumpy-sv-calling"
