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'])
