0), env.get('barcodesplit_filter_minreads', 0), env['DIR_BC_FILES'], os.path.join("barcodeList.txt"), os.path.join(env['BASECALLER_RESULTS'], "barcodeMask.bin"), env['libraryName'], env['sample'], env['site_name'], env['notes'], env['start_time'], env['chipType'], env['expName'], env['resultsName'], env['pgmName']) add_status("Basecaller", 0) except: traceback.print_exc() add_status("Basecaller", 1) set_result_status('Post Basecalling') try: basecaller.post_basecalling(env['BASECALLER_RESULTS'], env['expName'], env['resultsName'], env['flows']) add_status("PostBasecaller", 0) except: traceback.print_exc() add_status("PostBasecaller", 1) if not isProtonBlock: set_result_status('Merge Barcoded Basecaller Bams') try: basecaller.merge_barcoded_basecaller_bams( os.path.join(env['BASECALLER_RESULTS'], 'unfiltered.untrimmed')) add_status("MergeBarcodedBasecallerBamsUntrimmed", 0) except: traceback.print_exc()
env['notes'], env['start_time'], env['chipType'], env['expName'], env['resultsName'], env['pgmName'] ) add_status("Basecaller", 0) except: traceback.print_exc() add_status("Basecaller", 1) set_result_status('Post Basecalling') try: basecaller.post_basecalling(env['BASECALLER_RESULTS'],env['expName'],env['resultsName'],env['flows']) add_status("PostBasecaller", 0) except: traceback.print_exc() add_status("PostBasecaller", 1) if not isProtonBlock: set_result_status('Merge Barcoded Basecaller Bams') try: basecaller.merge_barcoded_basecaller_bams(os.path.join(env['BASECALLER_RESULTS'],'unfiltered.untrimmed')) add_status("MergeBarcodedBasecallerBamsUntrimmed", 0) except: traceback.print_exc() add_status("MergeBarcodedBasecallerBamsUntrimmed", 1) try: basecaller.merge_barcoded_basecaller_bams(os.path.join(env['BASECALLER_RESULTS'],'unfiltered.trimmed'))
f.write('basecalling = green\n') f.write('sffread = yellow\n') f.write('alignment = grey') f.close() generate_beadsummary=True skipsfftrim=True basecaller.post_basecalling( libsff_path, env['reverse_primer_dict'], skipsfftrim, env['sfftrim_args'], env['libraryKey'], env['flowOrder'], env['barcodeId'], env['barcodesplit_filter'], env['DIR_BC_FILES'], os.path.join("barcodeList.txt"), os.path.join(env['SIGPROC_RESULTS'], "bfmask.bin"), os.path.join(env['BASECALLER_RESULTS'], "barcodeMask.bin"), generate_beadsummary, env['BASECALLER_RESULTS']) basecaller.tf_processing( env['SIGPROC_RESULTS'], tfsff_path, env['libraryKey'], env['tfKey'], env['flowOrder'], env['BASECALLER_RESULTS'])