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(
