def stringtie_merge(*samples): to_merge = filter_missing(flatten([dd.get_assembled_gtf(data) for data in dd.sample_data_iterator(samples)])) data = samples[0][0] ref_file = dd.get_sam_ref(data) gtf_file = dd.get_gtf_file(data) num_cores = dd.get_num_cores(data) merged_gtf = stringtie.merge(to_merge, ref_file, gtf_file, num_cores, data) updated_samples = [] for data in dd.sample_data_iterator(samples): data = dd.set_merged_gtf(data, merged_gtf) updated_samples.append([data]) return updated_samples