for unfiltered_directory in [ os.path.join(env['BASECALLER_RESULTS'],'unfiltered.untrimmed'), os.path.join(env['BASECALLER_RESULTS'],'unfiltered.trimmed') ]: try: if os.path.exists(unfiltered_directory): unfiltered_basecaller_meta_information = None unfiltered_basecaller_datasets = blockprocessing.get_datasets_basecaller(unfiltered_directory) # TODO, don't generate this file if env['barcodeId']: basecaller.merge_barcoded_basecaller_bams( unfiltered_directory, unfiltered_basecaller_datasets, 'picard') if reference_selected: alignment.process_datasets( dirs, env['alignmentArgs'], env['ionstatsArgs'], unfiltered_directory, unfiltered_basecaller_meta_information, env['libraryKey'], graph_max_x, unfiltered_basecaller_datasets, unfiltered_directory, env['realign'], env['mark_duplicates'],
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')) add_status("MergeBarcodedBasecallerBamsTrimmed", 0) except: traceback.print_exc() add_status("MergeBarcodedBasecallerBamsTrimmed", 1) try: basecaller.merge_barcoded_basecaller_bams(env['BASECALLER_RESULTS']) add_status("MergeBarcodedBasecallerBams", 0) except: traceback.print_exc()
os.path.join(env["BASECALLER_RESULTS"], "unfiltered.trimmed"), ]: try: if os.path.exists(unfiltered_directory): unfiltered_basecaller_meta_information = None unfiltered_basecaller_datasets = blockprocessing.get_datasets_basecaller( unfiltered_directory) # TODO, don't generate this file if env["barcodeId"]: basecaller.merge_barcoded_basecaller_bams( unfiltered_directory, unfiltered_basecaller_datasets, "picard", ) if reference_selected: alignment.process_datasets( dirs, env["alignmentArgs"], env["ionstatsArgs"], unfiltered_directory, unfiltered_basecaller_meta_information, env["libraryKey"], graph_max_x, unfiltered_basecaller_datasets, unfiltered_directory, env["realign"],
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')) add_status("MergeBarcodedBasecallerBamsTrimmed", 0) except: traceback.print_exc() add_status("MergeBarcodedBasecallerBamsTrimmed", 1) try: basecaller.merge_barcoded_basecaller_bams(