def requires(self): if self.matched_n != '': return [ bam_processing.index_bam(sample=self.case + '_T', fastq_file=self.tumor, project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg), bam_processing.index_bam(sample=self.case + '_N', fastq_file=self.matched_n, project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg), msings_baseline(project_dir=self.project_dir, max_threads=self.max_threads, case_dict=self.case_dict, cfg=self.cfg) ] else: return [ bam_processing.index_bam(sample=self.case + '_T', fastq_file=self.tumor, project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg), msings_baseline(project_dir=self.project_dir, max_threads=self.max_threads, case_dict=self.case_dict, cfg=self.cfg) ]
def test_index_bam(): # sort so you can index output_fp = bp.create_sorted_bam(INPUT_BAM) bp.index_bam(output_fp) assert os.path.isfile(INPUT_BAM + '.bai')
def requires(self): return [ somatic_vcf_intersection(case=self.case, tumor=self.tumor, matched_n=self.matched_n, vcf_path=self.vcf_path, project_dir=self.project_dir, max_threads=self.max_threads, case_dict=self.case_dict, cfg=self.cfg), bam_processing.index_bam(sample=self.case + '_T', fastq_file=self.tumor, project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg) ]
def requires(self): # if self.matched_n != '': # return [bam_processing.index_bam(sample=self.case + '_T', fastq_file=self.tumor, project_dir=self.project_dir, max_threads=self.max_threads), bam_processing.index_bam(sample=self.case + '_N', fastq_file=self.matched_n, project_dir=self.project_dir, max_threads=self.max_threads)] # else: return bam_processing.index_bam(sample=self.sample, fastq_file=self.fastq_file, project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg)
def requires(self): # return bam_processing.index_bam(sample=self.case + '_T', fastq_file=self.tumor, project_dir=self.project_dir, max_threads=self.max_threads) return [ bam_processing.index_bam(sample=case_name + '_N', fastq_file=self.case_dict[case_name]['N'], project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg) for case_name in self.case_dict if self.case_dict[case_name]['N'] != '' ]
def requires(self): requirements = [ cnvkit_prep(max_threads=self.max_threads, project_dir=self.project_dir, cfg=self.cfg, case_dict=self.case_dict) ] if self.case_dict[self.case]['N'] != '': return requirements + [ bam_processing.index_bam( sample=self.case + '_T', fastq_file=self.case_dict[self.case]['T'], project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg), bam_processing.index_bam( sample=self.case + '_N', fastq_file=self.case_dict[self.case]['N'], project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg) ] #, variant_calling.mutect_pon(case_dict=self.case_dict, project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg)]
sample=self.case + '_T', fastq_file=self.case_dict[self.case]['T'], project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg), bam_processing.index_bam( sample=self.case + '_N', fastq_file=self.case_dict[self.case]['N'], project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg) ] #, variant_calling.mutect_pon(case_dict=self.case_dict, project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg)] else: return requirements + [ bam_processing.index_bam( sample=self.case + '_T', fastq_file=self.case_dict[self.case]['T'], project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg) ] #, variant_calling.mutect_pon(case_dict=self.case_dict, project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg)] def output(self): tumor_out = [ luigi.LocalTarget( os.path.join(self.project_dir, 'output', 'cnvkit', 'coverage', '%s_T.targetcoverage.cnn' % self.case)), luigi.LocalTarget( os.path.join(self.project_dir, 'output', 'cnvkit', 'coverage', '%s_T.antitargetcoverage.cnn' % self.case)) ]
def requires(self): return bam_processing.index_bam(sample=self.case + '_T', fastq_file=self.tumor, project_dir=self.project_dir, max_threads=self.max_threads, cfg=self.cfg)