def write_from_list()

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

• 24 lines of code
• 10 McCabe index (conditional complexity)

    def write_from_list(self, extension, list_r1, list_r2, workflow_name, library_type, sample_libtype=None,
                        sample_master=None, sample_names=None):
        files = []
        for i, f in enumerate(list_r1):
            sample_dir = os.path.dirname(list_r1[i])
            self.sample_name = sample_names[i] if sample_names is not None and sample_names[i].strip() \
                else get_sample_name(f, sample_dir)
            if self.read_type == 'paired' and self.parameter_type == "fastqFile":
                if 'None' in list_r2:
                    print('The comma-delimited fastq file list for R2 is required for paired mode.')
                    sys.exit(2)
                if len(list_r2) != len(list_r1):
                    print('The comma-delimited fastq file lists for R1 and R2 are not the same size.')
                    sys.exit(2)
                if sample_libtype is None:
                    self.add_sample(files, f, list_r2[i])
                else:
                    self.add_sample(files, f, list_r2[i], libtype=sample_libtype[i], master=sample_master[i])
            else:
                if sample_libtype is None:
                    self.add_sample(files, f, None)
                else:
                    self.add_sample(files, f, None, libtype=sample_libtype[i], master=sample_master[i])
        return self.write(extension, files, workflow_name, library_type, sample_libtype=sample_libtype)