def run(self): super(JobContigger, self).run() if not os.path.isdir(self.work_dir): os.mkdir(self.work_dir) logger.info("Generating contigs") repeat.generate_contigs(self.args, Job.run_params, self.repeat_graph_edges, self.work_dir, self.log_file, self.args.asm_config, self.repeat_graph, self.reads_alignment)
def run(self): super(JobContigger, self).run() if not os.path.isdir(self.work_dir): os.mkdir(self.work_dir) logger.info("Generating contigs") repeat.generate_contigs(self.args, Job.run_params, self.repeat_graph_edges, self.work_dir, self.log_file, self.args.asm_config, self.repeat_graph, self.reads_alignment) if os.path.getsize(self.out_files["contigs"]) == 0: raise asm.AssembleException("No contigs were assembled - " "pipeline stopped")