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"