def test_no_sample_name(self):
"""
Throws an exception if the Data portion has no Sample_Name column.
"""
stub_sample_sheet = """
[Header]
IEMFileVersion,3
Investigator Name,RL
Project Name,11-Jul-2014_nosamplenametest
Experiment Name,11-Jul-2014_nosamplenametest
Date,07/11/2014
Workflow,GenerateFASTQ
Assay,Nextera
Description,Nextera
Chemistry,Amplicon
[Reads]
251
251
[Settings]
[Data]
There,Is,No,Sample,Name
A,B,C,D,E
"""
with self.assertRaises(ValueError) as assertion:
sample_sheet_parser(StringIO(stub_sample_sheet))
self.assertEqual("sample sheet data header does not include Sample_Name",
assertion.exception.args[0])
def test_no_sample_name(self):
"""
Throws an exception if the Data portion has no Sample_Name column.
"""
stub_sample_sheet = """
[Header]
IEMFileVersion,3
Investigator Name,RL
Project Name,11-Jul-2014_nosamplenametest
Experiment Name,11-Jul-2014_nosamplenametest
Date,07/11/2014
Workflow,GenerateFASTQ
Assay,Nextera
Description,Nextera
Chemistry,Amplicon
[Reads]
251
251
[Settings]
[Data]
There,Is,No,Sample,Name
A,B,C,D,E
"""
with self.assertRaises(ValueError) as assertion:
sample_sheet_parser(StringIO(stub_sample_sheet))
self.assertEqual("sample sheet data header does not include Sample_Name",
assertion.exception.args[0])
def process_run(self, run_folder: Path):
if not (run_folder / 'needsprocessing').exists():
return False
if (run_folder / 'errorprocessing').exists():
return True
sample_sheet_path = run_folder / 'SampleSheet.csv'
folder_name = run_folder.name
with sample_sheet_path.open() as f:
try:
run_info = sample_sheet_parser(f)
except Exception:
raise RuntimeError(f'Failed to process run {folder_name}.')
project_groups = defaultdict(list)
for sample_info in run_info['DataSplit']:
sample_number = sample_info['sample_number']
project = sample_info['project']
project_groups[sample_number].append(project)
for project_names in project_groups.values():
project_names.sort()
name_tuple = tuple(project_names)
self.project_counts[name_tuple] += 1
self.latest_dates[name_tuple] = max(self.latest_dates[name_tuple],
folder_name)
top_projects = self.project_counts.most_common(3)
summary = ', '.join(f'({", ".join(project_codes)}): {count}'
for project_codes, count in top_projects)
logger.debug('After %s, top counts are: %s', folder_name, summary)
return True
def find_groups(file_names, sample_sheet_path, included_projects=None):
""" Group HCV samples with their MIDI partners.
:param list[str] file_names: a list of FASTQ file names without paths
:param sample_sheet_path: path to the SampleSheet.csv file
:param included_projects: project codes to include, or None to include
all
"""
with open(sample_sheet_path) as sample_sheet_file:
run_info = sample_sheet_parser(sample_sheet_file)
midi_files = {
row['sample']: row['filename']
for row in run_info['DataSplit'] if row['project'] == 'MidHCV'
}
wide_names = {
row['filename']: row['sample']
for row in run_info['DataSplit'] if (row['project'] != 'MidHCV' and (
included_projects is None or row['project'] in included_projects))
}
trimmed_names = {
'_'.join(file_name.split('_')[:2]): file_name
for file_name in file_names
}
for trimmed_name, file_name in sorted(trimmed_names.items()):
sample_name = wide_names.get(trimmed_name)
if sample_name is None:
# Project was not included.
continue
midi_trimmed = midi_files.get(sample_name + 'MIDI')
midi_name = trimmed_names.get(midi_trimmed)
yield SampleGroup(sample_name, (file_name, midi_name))
def process_folder(result_folder, qai_server, qai_user, qai_password,
pipeline_version):
logger.info('Uploading data to Oracle from {}'.format(result_folder))
collated_conseqs = os.path.join(result_folder, 'conseq.csv')
collated_counts = os.path.join(result_folder, 'remap_counts.csv')
cascade = os.path.join(result_folder, 'cascade.csv')
coverage_scores = os.path.join(result_folder, 'coverage_scores.csv')
all_results_path, _ = os.path.split(os.path.normpath(result_folder))
run_path, _ = os.path.split(all_results_path)
sample_sheet_file = os.path.join(run_path, "SampleSheet.csv")
with open(sample_sheet_file, "rU") as f:
sample_sheet = sample_sheet_parser.sample_sheet_parser(f)
ok_sample_regions = load_ok_sample_regions(result_folder)
with qai_helper.Session() as session:
session.login(qai_server, qai_user, qai_password)
run = find_run(session, sample_sheet["Experiment Name"])
with open(collated_conseqs, "rU") as f:
conseqs = build_conseqs(f, run, sample_sheet, ok_sample_regions)
with open(coverage_scores, "rU") as f, \
open(collated_counts, "rU") as f2, \
open(cascade, "rU") as f3:
upload_review_to_qai(f, f2, f3, run, sample_sheet, conseqs,
session, pipeline_version)
def process_run(run_folder: Path, skip_mid_hcv: bool):
if not (run_folder / 'needsprocessing').exists():
return False
if (run_folder / 'errorprocessing').exists():
return True
sample_sheet_path = run_folder / 'SampleSheet.csv'
with sample_sheet_path.open() as f:
try:
run_info = sample_sheet_parser(f)
except Exception:
raise RuntimeError(f'Failed to process run {run_folder.name}.')
sample_names = set(run_info['Data'])
if skip_mid_hcv:
sample_names = {
sample_name
for sample_name in sample_names
if not re.match(r'.*MidHCV_S\d+$', sample_name)
}
cascade_path = run_folder / 'Results' / 'version_7.9' / 'cascade.csv'
with cascade_path.open() as f:
reader = DictReader(f)
cascade_samples = {row['sample'] for row in reader}
missing_samples = sample_names - cascade_samples
if missing_samples:
logger.error('Missing samples in run %s: %s', run_folder.name,
sorted(missing_samples))
return True
def test_no_index2(self):
"""
Throws an exception if the Data portion has no Sample_Name column.
"""
stub_sample_sheet = """
[Header]
IEMFileVersion,3
Investigator Name,RL
Project Name,11-Jul-2014_nosamplenametest
Experiment Name,11-Jul-2014_nosamplenametest
Date,07/11/2014
Workflow,GenerateFASTQ
Assay,Nextera
Description,Nextera
Chemistry,Amplicon
[Reads]
251
251
[Settings]
[Data]
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,index,Sample_Project,Description,GenomeFolder
CFE_SomeId_10-Jul-2014_N501_Sample1_Proj1,Sample1_Proj1,10-Jul-2014_testing,N/A,ACGTACGT,\
10-Jul-2014_testing,Research:Sample1_Proj1:TRUE Comments:Sample1_Proj1:thisiscommentone \
Disablecontamcheck:Sample1_Proj1:FALSE,
CFE_SomeId_10-Jul-2014_N501_Sample2_Proj2,Sample2_Proj2,10-Jul-2014_testing,N/A,AAAAGGGG,\
10-Jul-2014_testing,Research:Sample2_Proj2:FALSE Comments:Sample2_Proj2:thisiscommenttwo \
Chemistry:Sample2_Proj2:BreakingBad Disablecontamcheck:Sample2_Proj2:TRUE,
"""
ss = sample_sheet_parser(StringIO(stub_sample_sheet))
sample = ss['Data']['Sample1-Proj1_S1']
self.assertEqual('ACGTACGT', sample['index1'])
self.assertEqual('X', sample['index2'])
self.assertEqual('N501-X', sample['tags'])
def test_extra_commas(self):
"""
Throws an exception if the Data portion has no Sample_Name column.
"""
stub_sample_sheet = """
[Header],,,,,,,
IEMFileVersion,3,,,,,,,
Investigator Name,RL,,,,,,,
Project Name,10-Jul-2014,,,,,,,
Experiment Name,10-Jul-2014,,,,,,,
Date,07/10/2014,,,,,,,
Workflow,GenerateFASTQ,,,,,,,
Assay,Nextera,,,,,,,
Description,Nextera,,,,,,,
Chemistry,Amplicon,,,,,,,
[Reads],,,,,,,
251,,,,,,,
251,,,,,,,
[Settings],,,,,,,
[Data],,,,,,,
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,index,index2,Sample_Project,Description,GenomeFolder
CFE_SomeId_10-Jul-2014_N501-N701_Sample1_Proj1,Sample1_Proj1,10-Jul-2014_testing,N/A,ACGTACGT,TGCATGCA,\
10-Jul-2014_testing,Research:Sample1_Proj1:TRUE Comments:Sample1_Proj1:thisiscommentone \
Disablecontamcheck:Sample1_Proj1:FALSE,
CFE_SomeId_10-Jul-2014_N501-N702_Sample2_Proj2,Sample2_Proj2,10-Jul-2014_testing,N/A,AAAAGGGG,CCCCTTTT,\
10-Jul-2014_testing,Research:Sample2_Proj2:FALSE Comments:Sample2_Proj2:thisiscommenttwo \
Chemistry:Sample2_Proj2:BreakingBad Disablecontamcheck:Sample2_Proj2:TRUE,
"""
ss = sample_sheet_parser(StringIO(stub_sample_sheet))
self.assertEqual(ss["Experiment Name"], "10-Jul-2014")
def test_no_index2(self):
"""
Throws an exception if the Data portion has no Sample_Name column.
"""
stub_sample_sheet = """
[Header]
IEMFileVersion,3
Investigator Name,RL
Project Name,11-Jul-2014_nosamplenametest
Experiment Name,11-Jul-2014_nosamplenametest
Date,07/11/2014
Workflow,GenerateFASTQ
Assay,Nextera
Description,Nextera
Chemistry,Amplicon
[Reads]
251
251
[Settings]
[Data]
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,index,Sample_Project,Description,GenomeFolder
CFE_SomeId_10-Jul-2014_N501_Sample1_Proj1,Sample1_Proj1,10-Jul-2014_testing,N/A,ACGTACGT,\
10-Jul-2014_testing,Research:Sample1_Proj1:TRUE Comments:Sample1_Proj1:thisiscommentone \
Disablecontamcheck:Sample1_Proj1:FALSE,
CFE_SomeId_10-Jul-2014_N501_Sample2_Proj2,Sample2_Proj2,10-Jul-2014_testing,N/A,AAAAGGGG,\
10-Jul-2014_testing,Research:Sample2_Proj2:FALSE Comments:Sample2_Proj2:thisiscommenttwo \
Chemistry:Sample2_Proj2:BreakingBad Disablecontamcheck:Sample2_Proj2:TRUE,
"""
ss = sample_sheet_parser(StringIO(stub_sample_sheet))
sample = ss['Data']['Sample1-Proj1_S1']
self.assertEqual('ACGTACGT', sample['index1'])
self.assertEqual('X', sample['index2'])
self.assertEqual('N501-X', sample['tags'])
def test_extra_commas(self):
"""
Throws an exception if the Data portion has no Sample_Name column.
"""
stub_sample_sheet = """
[Header],,,,,,,
IEMFileVersion,3,,,,,,,
Investigator Name,RL,,,,,,,
Project Name,10-Jul-2014,,,,,,,
Experiment Name,10-Jul-2014,,,,,,,
Date,07/10/2014,,,,,,,
Workflow,GenerateFASTQ,,,,,,,
Assay,Nextera,,,,,,,
Description,Nextera,,,,,,,
Chemistry,Amplicon,,,,,,,
[Reads],,,,,,,
251,,,,,,,
251,,,,,,,
[Settings],,,,,,,
[Data],,,,,,,
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,index,index2,Sample_Project,Description,GenomeFolder
CFE_SomeId_10-Jul-2014_N501-N701_Sample1_Proj1,Sample1_Proj1,10-Jul-2014_testing,N/A,ACGTACGT,TGCATGCA,\
10-Jul-2014_testing,Research:Sample1_Proj1:TRUE Comments:Sample1_Proj1:thisiscommentone \
Disablecontamcheck:Sample1_Proj1:FALSE,
CFE_SomeId_10-Jul-2014_N501-N702_Sample2_Proj2,Sample2_Proj2,10-Jul-2014_testing,N/A,AAAAGGGG,CCCCTTTT,\
10-Jul-2014_testing,Research:Sample2_Proj2:FALSE Comments:Sample2_Proj2:thisiscommenttwo \
Chemistry:Sample2_Proj2:BreakingBad Disablecontamcheck:Sample2_Proj2:TRUE,
"""
ss = sample_sheet_parser(StringIO(stub_sample_sheet))
self.assertEqual(ss["Experiment Name"], "10-Jul-2014")
def process_run(self, run_folder: Path):
if not (run_folder / 'needsprocessing').exists():
return False
if (run_folder / 'errorprocessing').exists():
return True
sample_sheet_path = run_folder / 'SampleSheet.csv'
folder_name = run_folder.name
with sample_sheet_path.open() as f:
try:
run_info = sample_sheet_parser(f)
except Exception:
raise RuntimeError(f'Failed to process run {folder_name}.')
project_groups = defaultdict(list)
for sample_info in run_info['DataSplit']:
sample_number = sample_info['sample_number']
project = sample_info['project']
project_groups[sample_number].append(project)
for project_names in project_groups.values():
project_names.sort()
name_tuple = tuple(project_names)
self.project_counts[name_tuple] += 1
self.latest_dates[name_tuple] = max(self.latest_dates[name_tuple], folder_name)
top_projects = self.project_counts.most_common(3)
summary = ', '.join(f'({", ".join(project_codes)}): {count}'
for project_codes, count in top_projects)
logger.debug('After %s, top counts are: %s', folder_name, summary)
return True
def find_groups(file_names, sample_sheet_path, included_projects=None):
""" Group HCV samples with their MIDI partners.
:param list[str] file_names: a list of FASTQ file names without paths
:param sample_sheet_path: path to the SampleSheet.csv file
:param included_projects: project codes to include, or None to include
all
"""
with open(sample_sheet_path) as sample_sheet_file:
run_info = sample_sheet_parser(sample_sheet_file)
overrides_path = Path(sample_sheet_path).parent / 'SampleSheetOverrides.csv'
if overrides_path.exists():
with overrides_path.open() as overrides_file:
read_sample_sheet_overrides(overrides_file, run_info)
midi_hcv_code = 'MidHCV'
midi_files = {row['sample']: row['filename']
for row in run_info['DataSplit']
if row['project'] == midi_hcv_code}
wide_names = {row['filename']: (row['sample'], row['project'])
for row in run_info['DataSplit']
if (row['project'] != midi_hcv_code and
(included_projects is None or
row['project'] in included_projects))}
trimmed_names = {'_'.join(file_name.split('_')[:2]): file_name
for file_name in file_names}
unused_names = set(trimmed_names.values())
for trimmed_name, file_name in sorted(trimmed_names.items()):
sample_entry = wide_names.get(trimmed_name)
if sample_entry is None:
# Project was not included.
continue
sample_name, project_code = sample_entry
midi_trimmed = midi_files.get(sample_name + 'MIDI')
if midi_trimmed is None and sample_name.upper().endswith('WG'):
sample_name = sample_name[:-2]
midi_trimmed = midi_files.get(sample_name + 'MIDI')
midi_name = trimmed_names.get(midi_trimmed)
unused_names.discard(file_name)
unused_names.discard(midi_name)
midi_project = midi_name and midi_hcv_code
yield SampleGroup(sample_name,
(file_name, midi_name),
(project_code, midi_project))
if unused_names:
sample_names = {file_name: sample_name
for sample_name, file_name in midi_files.items()}
for trimmed_name, file_name in sorted(trimmed_names.items()):
if file_name in unused_names:
unused_names.discard(file_name)
sample_name = sample_names.get(trimmed_name)
if sample_name is not None:
yield SampleGroup(sample_name,
(file_name, None),
(midi_hcv_code, None))
def test_read_sample_sheet_overrides(tmpdir):
sample_sheet_path = Path(str(tmpdir)) / 'SampleSheet.csv'
overrides_path = sample_sheet_path.parent / 'SampleSheetOverrides.csv'
sample_sheet_path.write_text("""\
[Header]
IEMFileVersion,3
Investigator Name,RL
Project Name,10-Jul-2014_v1test
Experiment Name,10-Jul-2014_v1test
Date,07/10/2014
Workflow,GenerateFASTQ
Assay,Nextera
Description,Nextera
Chemistry,Amplicon
[Reads]
251
251
[Settings]
[Data]
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,index,index2,Sample_Project,Description,GenomeFolder
CFE_SomeId_10-Jul-2014_N501-N701_Sample1_Proj1,Sample1_Proj1,10-Jul-2014_testing,N/A,ACGTACGT,TGCATGCA,\
10-Jul-2014_testing,Research:Sample1_Proj1:TRUE Comments:Sample1_Proj1:thisiscommentone \
Disablecontamcheck:Sample1_Proj1:FALSE,
CFE_SomeId_10-Jul-2014_N501-N702_Sample2_Proj2,Sample2_Proj2,10-Jul-2014_testing,N/A,AAAAGGGG,CCCCTTTT,\
10-Jul-2014_testing,Research:Sample2_Proj2:FALSE Comments:Sample2_Proj2:thisiscommenttwo \
Chemistry:Sample2_Proj2:BreakingBad Disablecontamcheck:Sample2_Proj2:TRUE,
""")
overrides_path.write_text("""\
sample,project
Sample2-Proj2_S2,AltB
""")
with sample_sheet_path.open() as f:
run_info = sample_sheet_parser(f)
with overrides_path.open() as f:
read_sample_sheet_overrides(f, run_info)
sample_map = run_info['Data']
assert len(sample_map) == 2
split_rows = run_info['DataSplit']
assert len(split_rows) == 2
assert split_rows[0]['project'] == 'Proj1'
assert split_rows[1]['project'] == 'AltB'
def find(self, source_folder, qai_run_names=None):
""" Find matching samples in the source folder.
Puts all the sample names in self.fastq_paths.
:param str source_folder: the folder to search for samples that match
self.extract_num
:param set qai_run_names: a set to add the new run name to as it would
be formatted on QAI.
"""
run_path = os.path.join(source_folder, 'MiSeq', 'runs', self.run_name)
if os.path.exists(run_path):
self.run_name = run_path
else:
run_parts = str(self.run_name).split('.')
if len(run_parts) < 2:
run_parts.append('M01841')
format_string = '%d-%b-%y' if len(
run_parts[0]) == 9 else '%d-%b-%Y'
run_date = datetime.strptime(run_parts[0], format_string)
base_run_name = run_date.strftime('%y%m%d') + '_' + run_parts[1]
pattern = os.path.join(source_folder, 'MiSeq', 'runs',
base_run_name + '*', NEEDS_PROCESSING)
matches = glob(pattern)
if len(matches) != 1:
raise RuntimeError(
'Expected one match for {}, but found: {}'.format(
pattern, matches))
self.run_name = os.path.dirname(matches[0])
pattern = os.path.join(self.run_name, 'Data', 'Intensities',
'BaseCalls', self.extract_num + '*_R1_*')
matches = glob(pattern)
if len(matches) == 0:
raise RuntimeError('No matches found for ' + pattern)
matches.sort()
self.fastq_paths = matches
if qai_run_names is not None:
sample_sheet_path = os.path.join(self.run_name, 'SampleSheet.csv')
with open(sample_sheet_path) as f:
try:
sample_sheet = sample_sheet_parser(f)
except ValueError:
print(f'Bad sample sheet for {self.run_name}.')
else:
qai_run_name = sample_sheet['Project Name']
qai_run_names.add(qai_run_name)
def find_groups(file_names, sample_sheet_path, included_projects=None):
""" Group HCV samples with their MIDI partners.
:param list[str] file_names: a list of FASTQ file names without paths
:param sample_sheet_path: path to the SampleSheet.csv file
:param included_projects: project codes to include, or None to include
all
"""
with open(sample_sheet_path) as sample_sheet_file:
run_info = sample_sheet_parser(sample_sheet_file)
midi_files = {row['sample']: row['filename']
for row in run_info['DataSplit']
if row['project'] == 'MidHCV'}
wide_names = {row['filename']: row['sample']
for row in run_info['DataSplit']
if (row['project'] != 'MidHCV' and
(included_projects is None or
row['project'] in included_projects))}
trimmed_names = {'_'.join(file_name.split('_')[:2]): file_name
for file_name in file_names}
unused_names = set(trimmed_names.values())
for trimmed_name, file_name in sorted(trimmed_names.items()):
sample_name = wide_names.get(trimmed_name)
if sample_name is None:
# Project was not included.
continue
midi_trimmed = midi_files.get(sample_name + 'MIDI')
if midi_trimmed is None and sample_name.upper().endswith('WG'):
sample_name = sample_name[:-2]
midi_trimmed = midi_files.get(sample_name + 'MIDI')
midi_name = trimmed_names.get(midi_trimmed)
unused_names.discard(file_name)
unused_names.discard(midi_name)
yield SampleGroup(sample_name, (file_name, midi_name))
if unused_names:
sample_names = {file_name: sample_name
for sample_name, file_name in midi_files.items()}
for trimmed_name, file_name in sorted(trimmed_names.items()):
if file_name in unused_names:
unused_names.discard(file_name)
sample_name = sample_names.get(trimmed_name)
if sample_name is not None:
yield SampleGroup(sample_name, (file_name, None))
def process_folder(result_folder,
qai_server,
qai_user,
qai_password,
pipeline_version):
logger.info('Uploading data to Oracle from {}'.format(result_folder))
collated_conseqs = os.path.join(result_folder, 'conseq.csv')
collated_counts = os.path.join(result_folder, 'remap_counts.csv')
cascade = os.path.join(result_folder, 'cascade.csv')
coverage_scores = os.path.join(result_folder, 'coverage_scores.csv')
all_results_path, _ = os.path.split(os.path.normpath(result_folder))
run_path, _ = os.path.split(all_results_path)
sample_sheet_file = os.path.join(run_path, "SampleSheet.csv")
with open(sample_sheet_file, "rU") as f:
sample_sheet = sample_sheet_parser.sample_sheet_parser(f)
ok_sample_regions = load_ok_sample_regions(result_folder)
with qai_helper.Session() as session:
session.login(qai_server,
qai_user,
qai_password)
run = find_run(session, sample_sheet["Experiment Name"])
with open(collated_conseqs, "rU") as f:
conseqs = build_conseqs(f,
run,
sample_sheet,
ok_sample_regions)
with open(coverage_scores, "rU") as f, \
open(collated_counts, "rU") as f2, \
open(cascade, "rU") as f3:
upload_review_to_qai(f,
f2,
f3,
run,
sample_sheet,
conseqs,
session,
pipeline_version)
def setUp(self):
self.maxDiff = None
self.ss = sample_sheet_parser(StringIO.StringIO(self.stub_sample_sheet))
def setUp(self):
self.ss = sample_sheet_parser(StringIO(self.stub_sample_sheet))
def main():
comm = MPI.COMM_WORLD # @UndefinedVariable
process_rank = comm.Get_rank()
process_count = comm.Get_size()
args = parseOptions(comm)
log_file = "{}/pipeline{}.log".format(args.run_folder, process_rank)
logger = miseq_logging.init_logging(log_file,
file_log_level=logging.DEBUG,
console_log_level=logging.INFO)
logger.info('Start processing run %s, rank %d',
args.run_folder,
process_rank)
if args.mode is not None:
run_info = None
else:
with open(args.run_folder+'/SampleSheet.csv', 'rU') as sample_sheet:
logger.debug("sample_sheet_parser({})".format(sample_sheet))
run_info = sample_sheet_parser(sample_sheet)
args.mode = run_info['Description']
fastq_samples = []
fastq_files = glob(args.run_folder + '/*_R1_001.fastq')
for i, fastq in enumerate(fastq_files):
if i % process_count != process_rank:
# skip samples that are assigned to other worker processes
continue
sample_info = SampleInfo(fastq)
# verify this sample is in SampleSheet.csv
if run_info and sample_info.key not in run_info['Data']:
logger.error(
'{} not in SampleSheet.csv - cannot map this sample'.format(
sample_info.key))
continue
fastq_samples.append(sample_info)
def launch_callback(command):
logger.info("Launching {!r}".format(command))
worker = Worker(launch_callback=launch_callback,
working_path=args.run_folder,
are_temp_folders_deleted=are_temp_folders_deleted,
logger=logger)
if args.phase in ('filter', 'all'):
filter_quality(args.run_folder, worker)
if args.phase in ('mapping', 'all'):
map_samples(args.run_folder, fastq_samples, worker)
if args.phase in ('counting', 'all'):
count_samples(fastq_samples, worker, args)
if args.phase in ('summarizing', 'all') and process_rank == 0:
collate_results(fastq_samples, worker, args, logger)
# FIXME: this log message gets sent before workers start
logger.info('Finish processing run %s, rank %d',
args.run_folder,
process_rank)
def setUp(self):
self.ss = sample_sheet_parser(StringIO(self.stub_sample_sheet))
def setUp(self):
self.maxDiff = None
self.ss = sample_sheet_parser(StringIO.StringIO(self.stub_sample_sheet))
