def write_from_dir()

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

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

    def write_from_dir(self, extension, sample_dir, sample_files, workflow_name, library_type):
        files = []
        for f in sample_files:
            self.sample_name = get_sample_name(f, sample_dir)
            parameter1 = join(sample_dir, f)
            if self.read_type == 'paired' and self.parameter_type == "fastqFile":
                parameter2 = join(sample_dir, f.replace('R1', 'R2'))
                if not exists(parameter2):
                    print("{} fastq file for paired mode is not found".format(parameter2))
                    sys.exit(2)
                self.add_sample(files, parameter1, parameter2)
            else:
                self.add_sample(files, parameter1, None)
        return self.write(extension, files, workflow_name, library_type)