def write()

in src/main/scripts/model/sample_manifest.py [0:0]

• 20 lines of code
• 5 McCabe index (conditional complexity)

    def write(self, extension, files, workflow_name, library_type, sample_libtype=None):
        data = {
            "parameter_type": self.parameter_type,
            "files": files,
            "libtype": True if sample_libtype is not None else False,
            "tab": '\t'
        }
        sample_type = 'Fastq' if extension.split('.')[0] == 'fastq' else 'Bam'
        main_dir = os.path.dirname(os.path.realpath(__import__("__main__").__file__))
        env = Environment(loader=FileSystemLoader("{}/config_templates/templates".format(main_dir)), trim_blocks=True,
                          lstrip_blocks=True)
        template = "sample_manifest_paired_template.txt" \
            if self.read_type == 'paired' and self.parameter_type == "fastqFile" \
            else "sample_manifest_single_template.txt"
        global_template = env.get_template(template)
        list_path = "{}_{}_Sample{}Paths.txt".format(workflow_name, library_type, sample_type)
        with open(list_path, "w") as f:
            f.write(global_template.render(data))
            f.close()

        return "{}/{}".format(os.getcwd(), list_path)