def main(args, outs):
specs = args.specs
runinfo_path = tk_preflight.check_runinfo_xml(args.run_path)
output_dir = os.path.dirname(outs.samplesheet)
csv_specs = [spec for spec in specs if spec.get('csv')]
if not csv_specs:
csv_path = make_csv_from_specs(specs, runinfo_path, output_dir)
outs.input_samplesheet = None
else:
csv_path = csv_specs[0]['csv']
shutil.copy(csv_path, outs.input_samplesheet)
read_info, flowcell = tk_bcl.load_run_info(runinfo_path)
(rta_version, rc_i2_read,
bcl_params) = tk_bcl.get_rta_version(args.run_path)
read_info_by_read_type = {r['read_name']: r for r in read_info}
r1_length = read_info_by_read_type.get('R1',
{'read_length': 0})['read_length']
r2_length = read_info_by_read_type.get('R2',
{'read_length': 0})['read_length']
rc_sample_index = (args.si_read_type == 'I2' and rc_i2_read)
lane_count = tk_lane.get_flowcell_lane_count(runinfo_path)
output_info = tk_sheet.transform_samplesheet(
csv_path,
outs.samplesheet,
flowcell_lane_count=lane_count,
r1_read_length=r1_length,
r2_read_length=r2_length,
rc_sample_index=rc_sample_index,
project_name=args.project)
outs.dual_indexed_samplesheet = output_info['dual_indexed']
def main(args, outs):
hostname = socket.gethostname()
print "Checking run folder..."
tk_preflight.check_rta_complete(args.run_path)
print "Checking RunInfo.xml..."
runinfo = tk_preflight.check_runinfo_xml(args.run_path)
if not args.allow_no_barcodes:
ok, msg = check_reads(runinfo)
if not ok:
martian.exit(msg)
print "Checking system environment..."
ok, msg = tk_preflight.check_ld_library_path()
if not ok:
martian.exit(msg)
# Presence of SampleSheet.csv interferes with demux.
# Ask customer to move it. Under older RTA, bcl2fastq looks for it
# in Data/Intensities/BaseCalls while under newer RTA, it looks for it
# at the top of the run folder.
bc_dir = os.path.join(args.run_path, "Data", "Intensities", "BaseCalls")
for ss_dir in [args.run_path, bc_dir]:
ilmn_sample_sheet = os.path.join(ss_dir, "SampleSheet.csv")
external = True
try:
import kitten
external = False
except ImportError:
pass
if external and os.path.exists(ilmn_sample_sheet):
martian.exit(
"On machine: %s, SampleSheet.csv found in run folder that would interfere with demux:\n%s\nPlease move, rename, or delete the file and run demux again."
% (hostname, ilmn_sample_sheet))
if args.check_executables:
print "Checking bcl2fastq..."
# Determine the RTA version of the run and whether this instrument
# requires i2 to RC'd
(rta_version, rc_i2_read,
bcl_params) = tenkit.bcl.get_rta_version(args.run_path)
martian.log_info("RTA Version: %s" % rta_version)
martian.log_info("BCL Params: %s" % str(bcl_params))
# Determine the best available bcl2fastq version to use
# Will call martian.exit() with an error message if there isn't
# a compatible version available
(major_ver,
full_ver) = tenkit.bcl.check_bcl2fastq(hostname, rta_version)
martian.log_info("Running bcl2fastq mode: %s. Version: %s" %
(major_ver, full_ver))
ok, msg = tk_preflight.check_open_fh()
if not ok:
martian.exit(msg)
def main(args, outs):
hostname = socket.gethostname()
print "Checking run folder..."
tk_preflight.check_rta_complete(args.run_path)
print "Checking RunInfo.xml..."
tk_preflight.check_runinfo_xml(args.run_path)
print "Checking system environment..."
ok, msg = tk_preflight.check_ld_library_path()
if not ok:
martian.exit(msg)
print "Checking barcode whitelist..."
tk_preflight.check_barcode_whitelist(args.barcode_whitelist)
if args.check_executables:
print "Checking bcl2fastq..."
(rta_version, rc_i2_read, bcl_params) = tk_bcl.get_rta_version(args.run_path)
martian.log_info("RTA Version: %s" % rta_version)
martian.log_info("BCL Params: %s" % str(bcl_params))
(major_ver, full_ver) = tk_bcl.check_bcl2fastq(hostname, rta_version)
martian.log_info("Running bcl2fastq mode: %s. Version: %s" % (major_ver, full_ver))
ok, msg = tk_preflight.check_open_fh()
if not ok:
martian.exit(msg)
if args.output_path is not None:
tk_preflight.check_folder_or_create("--output-dir", args.output_path, hostname, permission=os.W_OK|os.X_OK)
if args.interop_output_path is not None:
tk_preflight.check_folder_or_create("--interop-dir", args.interop_output_path, hostname, permission=os.W_OK|os.X_OK)
if args.max_bcl2fastq_threads < 1:
msg = "Cannot run bcl2fastq with zero threads."
martian.exit(msg)
def main(args, outs):
hostname = socket.gethostname()
print "Checking run folder..."
tk_preflight.check_rta_complete(args.run_path)
print "Checking RunInfo.xml..."
runinfo = tk_preflight.check_runinfo_xml(args.run_path)
print "Checking system environment..."
ok, msg = tk_preflight.check_ld_library_path()
if not ok:
martian.exit(msg)
print "Checking barcode whitelist..."
tk_preflight.check_barcode_whitelist(args.barcode_whitelist)
if args.check_executables:
print "Checking bcl2fastq..."
(rta_version, rc_i2_read,
bcl_params) = tk_bcl.get_rta_version(args.run_path)
martian.log_info("RTA Version: %s" % rta_version)
martian.log_info("BCL Params: %s" % str(bcl_params))
(major_ver, full_ver) = tk_bcl.check_bcl2fastq(hostname, rta_version)
martian.log_info("Running bcl2fastq mode: %s. Version: %s" %
(major_ver, full_ver))
if '--no-lane-splitting' in args.bcl2fastq2_args:
martian.exit("The --no-lane-splitting option is not supported.")
print "Emitting run information..."
martian.log_info("-------mkfastq diagnostic start-------")
emit_info(args)
print "Checking read specification..."
check_read_params(args, runinfo)
martian.log_info("-------mkfastq diagnostic end-------")
print "Checking samplesheet specs..."
check_specs(args)
print "Checking for dual index flowcell..."
check_dual_index(args, runinfo)
ok, msg = tk_preflight.check_open_fh()
if not ok:
martian.exit(msg)