if status == 'corrected': bidirectional = True else: bidirectional = False alignment.alignment( sff_path, fastq_path, align_full, DIR_BC_FILES, libraryName, sample, chipType, site_name, flows, notes, barcodeId, aligner_opts_extra, mark_duplicates, start_time, env['ALIGNMENT_RESULTS'], bidirectional, sam_parsed ) try: quality = os.path.join('.',"quality.summary") shutil.copy(quality, "../"+status+".quality.summary") except: printtime("ERROR: %s doesn't exist" % quality)
try: unfiltered_fastq = glob.glob("*." + status + ".fastq")[0] except: printtime("ERROR: unfiltered fastq file not found") unfiltered_fastq = "" alignment.alignment( unfiltered_sff, unfiltered_fastq, env['align_full'], env['DIR_BC_FILES'], env['libraryName'], env['sample'], env['chipType'], env['site_name'], env['flows'], env['notes'], env['barcodeId'], env['aligner_opts_extra'], env['start_time'], env['ALIGNMENT_RESULTS'], bidirectional, env['sam_parsed']) os.chdir(top_dir) else: printtime("Directory unfiltered does not exist") alignment.alignment(