call_fastqc(self.dir_info.second, self.dir_info.fastqc_output_dir) except: raise Exception("Couldn't deduplicate for mate " + self.name() + "! Please inspect the log file") def call_trim_galore(self): try: trimmer = TrimGalore(self.dir_info.first, self.dir_info.second, self.dir_info.trim_galore_output_dir) run_shell_command(trimmer.generate_command()) except: raise Exception("Couldn't trim galore for mate " + self.name() + "! Please inspect the log file") def pipeline(self, clean_output_dir=True): self.setup(clean_output_dir) self.call_fastqc() self.call_trim_galore() self.call_bismark() self.call_deduplicate() ##self.extract_methylation() def clean(self): raise NotImplementedError() if __name__ == "__main__": handler = MateHandler() test_mate = handler.get_mate_by_name("S112_tag_6_GCCAAT_L003_14101") pipeline = MatePipeline(test_mate) pipeline.pipeline()