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()
add_status("MergeBarcodedBasecallerBams", 1)
set_result_status('TF Processing')
try:
basecaller.tf_processing(
os.path.join(env['BASECALLER_RESULTS'],
"rawtf.basecaller.bam"), env['tfKey'],
env['flowOrder'], env['BASECALLER_RESULTS'], '.')
add_status("TF Processing", 0)
except:
traceback.print_exc()
add_status("TF Processing", 1)
##################################################
# Unfiltered BAM
##################################################
if not isProtonBlock:
try:
if os.path.exists(
os.path.join(env['BASECALLER_RESULTS'],
'unfiltered.untrimmed')):
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()
add_status("MergeBarcodedBasecallerBams", 1)
set_result_status('TF Processing')
try:
basecaller.tf_processing(
os.path.join(env['BASECALLER_RESULTS'], "rawtf.basecaller.bam"),
env['tfKey'],
env['flowOrder'],
env['BASECALLER_RESULTS'],
'.')
add_status("TF Processing", 0)
except:
traceback.print_exc()
add_status("TF Processing", 1)
##################################################
# Unfiltered BAM
##################################################
if not isProtonBlock:
try:
if os.path.exists(os.path.join(env['BASECALLER_RESULTS'],'unfiltered.untrimmed')):
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'])
##################################################
# Unfiltered SFF
##################################################
top_dir = os.getcwd()
try:
unfiltered_dir = "unfiltered"
if os.path.exists(unfiltered_dir):
#change to the unfiltered dir
os.chdir(os.path.join(top_dir,unfiltered_dir))
