try: os.mkdir( os.path.join(env["BASECALLER_RESULTS"], "unfiltered.untrimmed")) basecaller.merge_datasets_basecaller_json( dirs, os.path.join(env["BASECALLER_RESULTS"], "unfiltered.untrimmed"), ) blockprocessing.merge_bams( dirs, os.path.join(env["BASECALLER_RESULTS"], "unfiltered.untrimmed"), basecaller_datasets, "picard", ) except Exception: print(traceback.format_exc()) try: os.mkdir( os.path.join(env["BASECALLER_RESULTS"], "unfiltered.trimmed")) basecaller.merge_datasets_basecaller_json( dirs, os.path.join(env["BASECALLER_RESULTS"], "unfiltered.trimmed"))
printtime("ERROR: merging rawtf.basecaller.bam unsuccessful") if do_unfiltered_processing: basecaller_datasets = blockprocessing.get_datasets_basecaller(env['BASECALLER_RESULTS']) try: os.mkdir(os.path.join(env['BASECALLER_RESULTS'],'unfiltered.untrimmed')) basecaller.merge_datasets_basecaller_json( dirs, os.path.join(env['BASECALLER_RESULTS'],"unfiltered.untrimmed")) blockprocessing.merge_bams( dirs, os.path.join(env['BASECALLER_RESULTS'],"unfiltered.untrimmed"), basecaller_datasets, 'picard') except: print traceback.format_exc() try: os.mkdir(os.path.join(env['BASECALLER_RESULTS'],'unfiltered.trimmed')) basecaller.merge_datasets_basecaller_json( dirs, os.path.join(env['BASECALLER_RESULTS'],"unfiltered.trimmed")) blockprocessing.merge_bams( dirs,
printtime("ERROR: merging rawtf.basecaller.bam unsuccessful") if do_unfiltered_processing: basecaller_datasets = blockprocessing.get_datasets_basecaller(env['BASECALLER_RESULTS']) try: os.mkdir(os.path.join(env['BASECALLER_RESULTS'], 'unfiltered.untrimmed')) basecaller.merge_datasets_basecaller_json( dirs, os.path.join(env['BASECALLER_RESULTS'], "unfiltered.untrimmed")) blockprocessing.merge_bams( dirs, os.path.join(env['BASECALLER_RESULTS'], "unfiltered.untrimmed"), basecaller_datasets, 'picard') except: print traceback.format_exc() try: os.mkdir(os.path.join(env['BASECALLER_RESULTS'], 'unfiltered.trimmed')) basecaller.merge_datasets_basecaller_json( dirs, os.path.join(env['BASECALLER_RESULTS'], "unfiltered.trimmed")) blockprocessing.merge_bams( dirs, os.path.join(env['BASECALLER_RESULTS'], "unfiltered.trimmed"),