def main():
"""main function
"""
parser = argparse.ArgumentParser(
description=__doc__.format(PIPELINE_NAME=PIPELINE_NAME, PIPELINE_VERSION=get_pipeline_version())
)
# generic args
parser.add_argument("-o", "--outdir", required=True, help="Output directory (may not exist)")
parser.add_argument("--name", help="Give this analysis run a name (used in email and report)")
parser.add_argument("--no-mail", action="store_true", help="Don't send mail on completion")
# site = get_site()
default = get_default_queue("slave")
parser.add_argument(
"-w", "--slave-q", default=default, help="Queue to use for slave jobs (default: {})".format(default)
)
default = get_default_queue("master")
parser.add_argument(
"-m", "--master-q", default=default, help="Queue to use for master job (default: {})".format(default)
)
parser.add_argument("-n", "--no-run", action="store_true")
parser.add_argument("-v", "--verbose", action="count", default=0, help="Increase verbosity")
parser.add_argument("-q", "--quiet", action="count", default=0, help="Decrease verbosity")
cfg_group = parser.add_argument_group("Configuration files (advanced)")
cfg_group.add_argument(
"--sample-cfg", help="Config-file (YAML) listing samples and readunits." " Collides with -1, -2 and -s"
)
for name, descr in [("references", "reference sequences"), ("params", "parameters"), ("modules", "modules")]:
default = os.path.abspath(os.path.join(CFG_DIR, "{}.yaml".format(name)))
cfg_group.add_argument(
"--{}-cfg".format(name),
default=default,
help="Config-file (yaml) for {}. (default: {})".format(descr, default),
)
# pipeline specific args
parser.add_argument(
"--normal-fq1",
nargs="+",
help="Normal FastQ file/s (gzip only)."
" Multiple input files supported (auto-sorted)."
" Note: each file (or pair) gets a unique read-group id."
" Collides with --sample-cfg.",
)
parser.add_argument("--normal-fq2", nargs="+", help="Normal FastQ file/s (if paired) (gzip only). See also --fq1")
parser.add_argument(
"--tumor-fq1",
nargs="+",
help="Tumor FastQ file/s (gzip only)."
" Multiple input files supported (auto-sorted)."
" Note: each file (or pair) gets a unique read-group id."
" Collides with --sample-cfg.",
)
parser.add_argument("--tumor-fq2", nargs="+", help="Tumor FastQ file/s (if paired) (gzip only). See also --fq1")
parser.add_argument("-t", "--seqtype", required=True, choices=["WGS", "WES", "targeted"], help="Sequencing type")
parser.add_argument(
"-l",
"--intervals",
help="Intervals file (e.g. bed file) listing regions of interest." " Required for WES and targeted sequencing.",
)
parser.add_argument("-D", "--dont-mark-dups", action="store_true", help="Don't mark duplicate reads")
parser.add_argument(
"--normal-bam",
help="Advanced: Injects normal BAM (overwrites normal-fq options)."
" WARNING: reference and postprocessing need to match pipeline requirements",
)
parser.add_argument(
"--tumor-bam",
help="Advanced: Injects tumor BAM (overwrites tumor-fq options)."
" WARNING: reference and postprocessing need to match pipeline requirements",
)
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10 * args.quiet - 10 * args.verbose)
aux_logger.setLevel(logging.WARN + 10 * args.quiet - 10 * args.verbose)
if os.path.exists(args.outdir):
logger.fatal("Output directory %s already exists", args.outdir)
sys.exit(1)
# samples is a dictionary with sample names as key (mostly just
# one) and readunit keys as value. readunits is a dict with
# readunits (think: fastq pairs with attributes) as value
if args.sample_cfg:
if any([args.normal_fq1, args.normal_fq2, args.tumor_fq1, args.tumor_fq2, args.normal_bam, args.tumor_bam]):
logger.fatal("Config file overrides fastq and sample input arguments." " Use one or the other")
sys.exit(1)
if not os.path.exists(args.sample_cfg):
logger.fatal("Config file %s does not exist", args.sample_cfg)
sys.exit(1)
samples, readunits = get_samples_and_readunits_from_cfgfile(args.sample_cfg)
else:
samples = dict()
if args.normal_bam:
normal_readunits = dict()
samples["normal"] = []
assert os.path.exists(args.normal_bam)
else:
if not all([args.normal_fq1, args.tumor_fq1]):
logger.fatal("Need at least fq1 and sample without config file")
sys.exit(1)
normal_readunits = get_readunits_from_args(args.normal_fq1, args.normal_fq2)
samples["normal"] = list(normal_readunits.keys())
if args.tumor_bam:
tumor_readunits = dict()
samples["tumor"] = []
assert os.path.exists(args.tumor_bam)
else:
tumor_readunits = get_readunits_from_args(args.tumor_fq1, args.tumor_fq2)
samples["tumor"] = list(tumor_readunits.keys())
readunits = dict(normal_readunits)
readunits.update(tumor_readunits)
assert sorted(samples) == sorted(["normal", "tumor"])
# FIXME howt to
# if not os.path.exists(reffa):
# logger.fatal("Reference '%s' doesn't exist", reffa)
# sys.exit(1)
#
# for p in ['bwa', 'samtools']:
# if not ref_is_indexed(reffa, p):
# logger.fatal("Reference '%s' doesn't appear to be indexed with %s", reffa, p)
# sys.exit(1)
if args.seqtype in ["WES", "targeted"]:
if not args.intervals:
logger.fatal("Analysis of exome and targeted sequence runs requires a bed file")
sys.exit(1)
else:
if not os.path.exists(args.intervals):
logger.fatal("Intervals file %s does not exist", args.sample_cfg)
sys.exit(1)
logger.warning("Compatilibity between interval file and" " reference not checked") # FIXME
# turn arguments into user_data that gets merged into pipeline config
#
# generic data first
user_data = dict()
user_data["mail_on_completion"] = not args.no_mail
user_data["readunits"] = readunits
user_data["samples"] = samples
if args.name:
user_data["analysis_name"] = args.name
user_data["seqtype"] = args.seqtype
user_data["intervals"] = args.intervals
user_data["mark_dups"] = not args.dont_mark_dups
pipeline_handler = PipelineHandler(
PIPELINE_NAME,
PIPELINE_BASEDIR,
args.outdir,
user_data,
master_q=args.master_q,
slave_q=args.slave_q,
params_cfgfile=args.params_cfg,
modules_cfgfile=args.modules_cfg,
refs_cfgfile=args.references_cfg,
cluster_cfgfile=get_cluster_cfgfile(CFG_DIR),
)
pipeline_handler.setup_env()
# inject existing BAM by symlinking (everything upstream is temporary anyway)
for sample, bam in [("normal", args.normal_bam), ("tumor", args.tumor_bam)]:
if bam:
# target as defined in Snakefile!
target = os.path.join(args.outdir, "out", sample, "{}.bwamem.lofreq.dedup.lacer.bam".format(sample))
os.makedirs(os.path.dirname(target))
os.symlink(os.path.abspath(bam), target)
pipeline_handler.submit(args.no_run)
def main():
"""main function
"""
parser = argparse.ArgumentParser(description=__doc__.format(
PIPELINE_NAME=PIPELINE_NAME, PIPELINE_VERSION=get_pipeline_version()))
# generic args
parser.add_argument('-o', "--outdir", required=True,
help="Output directory (must not exist)")
parser.add_argument('--name',
help="Give this analysis run a name (used in email and report)")
parser.add_argument('--no-mail', action='store_true',
help="Don't send mail on completion")
#site = get_site()
default = get_default_queue('slave')
parser.add_argument('-w', '--slave-q', default=default,
help="Queue to use for slave jobs (default: {})".format(default))
default = get_default_queue('master')
parser.add_argument('-m', '--master-q', default=default,
help="Queue to use for master job (default: {})".format(default))
parser.add_argument('-n', '--no-run', action='store_true')
parser.add_argument('-v', '--verbose', action='count', default=0,
help="Increase verbosity")
parser.add_argument('-q', '--quiet', action='count', default=0,
help="Decrease verbosity")
cfg_group = parser.add_argument_group('Configuration files (advanced)')
cfg_group.add_argument('--sample-cfg',
help="Config-file (YAML) listing samples and readunits."
" Collides with -1, -2 and -s")
for name, descr in [("references", "reference sequences"),
("params", "parameters"),
("modules", "modules")]:
default = os.path.abspath(os.path.join(CFG_DIR, "{}.yaml".format(name)))
cfg_group.add_argument('--{}-cfg'.format(name),
default=default,
help="Config-file (yaml) for {}. (default: {})".format(descr, default))
# pipeline specific args
parser.add_argument('-1', "--fq1", nargs="+",
help="FastQ file/s (gzip only)."
" Multiple input files supported (auto-sorted)."
" Note: each file (or pair) gets a unique read-group id."
" Collides with --sample-cfg.")
parser.add_argument('-2', "--fq2", nargs="+",
help="FastQ file/s (if paired) (gzip only). See also --fq1")
parser.add_argument('-s', "--sample",
help="Sample name. Collides with --sample-cfg.")
parser.add_argument('-C', "--cuffdiff", action='store_true',
dest="run_cuffdiff",
help="Also run cuffdiff")
parser.add_argument('-S', '--stranded', action='store_true',
help="Stranded library prep (default is unstranded)")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10*args.quiet - 10*args.verbose)
aux_logger.setLevel(logging.WARN + 10*args.quiet - 10*args.verbose)
if os.path.exists(args.outdir):
logger.fatal("Output directory %s already exists", args.outdir)
sys.exit(1)
# samples is a dictionary with sample names as key (mostly just
# one) and readunit keys as value. readunits is a dict with
# readunits (think: fastq pairs with attributes) as value
if args.sample_cfg:
if any([args.fq1, args.fq2, args.sample]):
logger.fatal("Config file overrides fastq and sample input arguments."
" Use one or the other")
sys.exit(1)
if not os.path.exists(args.sample_cfg):
logger.fatal("Config file %s does not exist", args.sample_cfg)
sys.exit(1)
samples, readunits = get_samples_and_readunits_from_cfgfile(args.sample_cfg)
else:
if not all([args.fq1, args.sample]):
logger.fatal("Need at least fq1 and sample without config file")
sys.exit(1)
readunits = get_readunits_from_args(args.fq1, args.fq2)
# all readunits go into this one sample specified on the command-line
samples = dict()
samples[args.sample] = list(readunits.keys())
# FIXME checks on reffa index (currently not exposed via args)
# turn arguments into user_data that gets merged into pipeline config
#
# generic data first
user_data = dict()
user_data['mail_on_completion'] = not args.no_mail
user_data['readunits'] = readunits
user_data['samples'] = samples
if args.name:
user_data['analysis_name'] = args.name
user_data['stranded'] = args.stranded
user_data['run_cuffdiff'] = args.run_cuffdiff
user_data['paired_end'] = any(ru.get('fq2') for ru in readunits.values())
if user_data['paired_end']:
assert all(ru.get('fq2') for ru in readunits.values()), (
"Can't handle mix of paired-end and single-end")
pipeline_handler = PipelineHandler(
PIPELINE_NAME, PIPELINE_BASEDIR,
args.outdir, user_data,
master_q=args.master_q,
slave_q=args.slave_q,
params_cfgfile=args.params_cfg,
modules_cfgfile=args.modules_cfg,
refs_cfgfile=args.references_cfg,
cluster_cfgfile=get_cluster_cfgfile(CFG_DIR))
pipeline_handler.setup_env()
pipeline_handler.submit(args.no_run)
def main():
"""main function
"""
parser = argparse.ArgumentParser(description=__doc__.format(
PIPELINE_NAME=PIPELINE_NAME, PIPELINE_VERSION=get_pipeline_version()))
# generic args
parser.add_argument('-o', "--outdir", required=True,
help="Output directory (may not exist)")
parser.add_argument('--name',
help="Give this analysis run a name (used in email and report)")
parser.add_argument('--no-mail', action='store_true',
help="Don't send mail on completion")
#site = get_site()
default = get_default_queue('slave')
parser.add_argument('-w', '--slave-q', default=default,
help="Queue to use for slave jobs (default: {})".format(default))
default = get_default_queue('master')
parser.add_argument('-m', '--master-q', default=default,
help="Queue to use for master job (default: {})".format(default))
parser.add_argument('-n', '--no-run', action='store_true')
parser.add_argument('-v', '--verbose', action='count', default=0,
help="Increase verbosity")
parser.add_argument('-q', '--quiet', action='count', default=0,
help="Decrease verbosity")
cfg_group = parser.add_argument_group('Configuration files (advanced)')
cfg_group.add_argument('--sample-cfg',
help="Config-file (YAML) listing samples and readunits."
" Collides with -1, -2 and -s")
for name, descr in [("references", "reference sequences"),
("params", "parameters"),
("modules", "modules")]:
default = os.path.abspath(os.path.join(CFG_DIR, "{}.yaml".format(name)))
cfg_group.add_argument('--{}-cfg'.format(name),
default=default,
help="Config-file (yaml) for {}. (default: {})".format(descr, default))
# pipeline specific args
parser.add_argument('-1', "--fq1", nargs="+",
help="FastQ file/s (gzip only)."
" Multiple input files supported (auto-sorted)."
" Note: each file (or pair) gets a unique read-group id."
" Collides with --sample-cfg.")
parser.add_argument('-2', "--fq2", nargs="+",
help="FastQ file/s (if paired) (gzip only). See also --fq1")
parser.add_argument('-s', "--sample",
help="Sample name. Collides with --sample-cfg.")
parser.add_argument('-t', "--seqtype", required=True,
choices=['WGS', 'WES', 'targeted'],
help="Sequencing type")
parser.add_argument('-l', "--intervals",
help="Intervals file (e.g. bed file) listing regions of interest."
" Required for WES and targeted sequencing.")
parser.add_argument('-D', '--dont-mark-dups', action='store_true',
help="Don't mark duplicate reads")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10*args.quiet - 10*args.verbose)
aux_logger.setLevel(logging.WARN + 10*args.quiet - 10*args.verbose)
if os.path.exists(args.outdir):
logger.fatal("Output directory %s already exists", args.outdir)
sys.exit(1)
# samples is a dictionary with sample names as key (mostly just
# one) and readunit keys as value. readunits is a dict with
# readunits (think: fastq pairs with attributes) as value
if args.sample_cfg:
if any([args.fq1, args.fq2, args.sample]):
logger.fatal("Config file overrides fastq and sample input arguments."
" Use one or the other")
sys.exit(1)
if not os.path.exists(args.sample_cfg):
logger.fatal("Config file %s does not exist", args.sample_cfg)
sys.exit(1)
samples, readunits = get_samples_and_readunits_from_cfgfile(args.sample_cfg)
else:
if not all([args.fq1, args.sample]):
logger.fatal("Need at least fq1 and sample without config file")
sys.exit(1)
readunits = get_readunits_from_args(args.fq1, args.fq2)
# all readunits go into this one sample specified on the command-line
samples = dict()
samples[args.sample] = list(readunits.keys())
# FIXME how to?
#for p in ['bwa', 'samtools']:
# if not ref_is_indexed(args.reffa, p):
# logger.fatal("Reference '%s' doesn't appear to be indexed with %s", args.reffa, p)
# sys.exit(1)
if args.seqtype in ['WES', 'targeted']:
if not args.intervals:
logger.fatal("Analysis of exome and targeted sequence runs requires a bed file")
sys.exit(1)
else:
if not os.path.exists(args.intervals):
logger.fatal("Intervals file %s does not exist", args.sample_cfg)
sys.exit(1)
logger.warning("Compatilibity between interval file and"
" reference not checked")# FIXME
# turn arguments into user_data that gets merged into pipeline config
#
# generic data first
user_data = dict()
user_data['mail_on_completion'] = not args.no_mail
user_data['readunits'] = readunits
user_data['samples'] = samples
if args.name:
user_data['analysis_name'] = args.name
user_data['seqtype'] = args.seqtype
user_data['intervals'] = args.intervals
user_data['mark_dups'] = not args.dont_mark_dups
pipeline_handler = PipelineHandler(
PIPELINE_NAME, PIPELINE_BASEDIR,
args.outdir, user_data,
master_q=args.master_q,
slave_q=args.slave_q,
params_cfgfile=args.params_cfg,
modules_cfgfile=args.modules_cfg,
refs_cfgfile=args.references_cfg,
cluster_cfgfile=get_cluster_cfgfile(CFG_DIR))
pipeline_handler.setup_env()
pipeline_handler.submit(args.no_run)
def main():
"""main function
"""
# FIXME ugly and code duplication in bcl2fastq_dbupdate.py
mongo_status_script = os.path.abspath(os.path.join(
os.path.dirname(sys.argv[0]), "mongo_status.py"))
assert os.path.exists(mongo_status_script)
parser = argparse.ArgumentParser(description=__doc__.format(
PIPELINE_NAME=PIPELINE_NAME, PIPELINE_VERSION=get_pipeline_version()))
parser.add_argument('-r', "--runid",
help="Run ID plus flowcell ID (clashes with -d)")
parser.add_argument('-d', "--rundir",
help="BCL input directory (clashes with -r)")
parser.add_argument('-o', "--outdir",
help="Output directory (must not exist; required if called by user)")
parser.add_argument('-t', "--testing", action='store_true',
help="Use MongoDB test server")
parser.add_argument('--no-archive', action='store_true',
help="Don't archieve this analysis")
parser.add_argument('--name',
help="Give this analysis run a name (used in email and report)")
parser.add_argument('--no-mail', action='store_true',
help="Don't send mail on completion")
default = get_default_queue('slave')
parser.add_argument('-w', '--slave-q', default=default,
help="Queue to use for slave jobs (default: {})".format(default))
default = get_default_queue('master')
parser.add_argument('-m', '--master-q', default=default,
help="Queue to use for master job (default: {})".format(default))
parser.add_argument('-l', '--lanes', type=int, nargs="*",
help="Limit run to given lane/s (multiples separated by space")
parser.add_argument('-i', '--mismatches', type=int,
help="Max. number of allowed barcode mismatches (0>=x<=2)"
" setting a value here overrides the default settings read from ELM)")
parser.add_argument('-n', '--no-run', action='store_true')
parser.add_argument('-v', '--verbose', action='count', default=0,
help="Increase verbosity")
parser.add_argument('-q', '--quiet', action='count', default=0,
help="Decrease verbosity")
cfg_group = parser.add_argument_group('Configuration files (advanced)')
for name, descr in [("modules", "modules")]:
default = os.path.abspath(os.path.join(CFG_DIR, "{}.yaml".format(name)))
cfg_group.add_argument('--{}-cfg'.format(name),
default=default,
help="Config-file (yaml) for {}. (default: {})".format(descr, default))
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10*args.quiet - 10*args.verbose)
aux_logger.setLevel(logging.WARN + 10*args.quiet - 10*args.verbose)
if args.mismatches is not None:
if args.mismatches > 2 or args.mismatches < 0:
logger.fatal("Number of mismatches must be between 0-2")
sys.exit(1)
lane_info = ''
lane_nos = []
if args.lanes:
lane_info = '--tiles '
for lane in args.lanes:
if lane > 8 or lane < 1:
logger.fatal("Lane number must be between 1-8")
sys.exit(1)
else:
lane_info += 's_{}'.format(lane)+','
lane_info = lane_info.rstrip()
lane_info = lane_info[:-1]
lane_nos = list(args.lanes)
if args.runid and args.rundir:
logger.fatal("Cannot use run-id and input directory arguments simultaneously")
sys.exit(1)
elif args.runid:
rundir = run_folder_for_run_id(args.runid)
elif args.rundir:
rundir = os.path.abspath(args.rundir)
else:
logger.fatal("Need either run-id or input directory")
sys.exit(1)
if not os.path.exists(rundir):
logger.fatal("Expected run directory %s does not exist", rundir)
logger.info("Rundir is %s", rundir)
if not args.outdir:
outdir = get_bcl2fastq_outdir(args.runid)
else:
outdir = args.outdir
if os.path.exists(outdir):
logger.fatal("Output directory %s already exists", outdir)
sys.exit(1)
# create now so that generate_bcl2fastq_cfg.py can run
os.makedirs(outdir)
# catch cases where rundir was user provided and looks weird
try:
_, runid, flowcellid = get_machine_run_flowcell_id(rundir)
run_num = runid + "_" + flowcellid
except:
run_num = "UNKNOWN-" + rundir.split("/")[-1]
# call generate_bcl2fastq_cfg
#
# FIXME ugly assumes same directory (just like import above). better to import and run main()?
generate_bcl2fastq = os.path.join(
os.path.dirname(sys.argv[0]), "generate_bcl2fastq_cfg.py")
assert os.path.exists(generate_bcl2fastq)
cmd = [generate_bcl2fastq, '-r', rundir, '-o', outdir]
if args.testing:
cmd.append("-t")
logger.debug("Executing %s", ' ' .join(cmd))
try:
res = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
except subprocess.CalledProcessError as e:
logger.fatal("The following command failed with return code %s: %s",
e.returncode, ' '.join(cmd))
logger.fatal("Output: %s", e.output.decode())
logger.fatal("Exiting")
sys.exit(1)
# generate_bcl2fastq is normally quiet. if there's output, make caller aware of it
# use sys instead of logger to avoid double logging
if res:
sys.stderr.write(res.decode())
# just created files
muxinfo_cfg = os.path.join(outdir, MUXINFO_CFG)
samplesheet_csv = os.path.join(outdir, SAMPLESHEET_CSV)
usebases_cfg = os.path.join(outdir, USEBASES_CFG)
# NOTE: signal for failed runs is exit 0 from generate_bcl2fastq and missing output files
#
if any([not os.path.exists(x) for x in [muxinfo_cfg, samplesheet_csv, usebases_cfg]]):
# one missing means all should be missing
assert all([not os.path.exists(x) for x in [muxinfo_cfg, samplesheet_csv, usebases_cfg]])
seqrunfailed(mongo_status_script, run_num, outdir, args.testing)
sys.exit(0)
# turn arguments into user_data that gets merged into pipeline config
user_data = {'rundir': rundir,
'lanes_arg': lane_info,
'samplesheet_csv': samplesheet_csv,
'no_archive': args.no_archive,
'mail_on_completion': not args.no_mail,
'run_num': run_num}
if args.name:
user_data['analysis_name'] = args.name
usebases_arg = ''
with open(usebases_cfg, 'r') as stream:
try:
d = yaml.load(stream)
assert 'usebases' in d
assert len(d) == 1# make sure usebases is only key
for ub in d['usebases']:
#print (ub)
usebases_arg += '--use-bases-mask {} '.format(ub)
#user_data = {'usebases_arg' : usebases_arg}
except yaml.YAMLError as exc:
logger.fatal(exc)
raise
user_data['usebases_arg'] = usebases_arg
os.unlink(usebases_cfg)
mux_units = get_mux_units_from_cfgfile(muxinfo_cfg, lane_nos)
if args.mismatches is not None:
mux_units = [mu._replace(barcode_mismatches=args.mismatches)
for mu in mux_units]
os.unlink(muxinfo_cfg)
user_data['units'] = dict()
for mu in mux_units:
# special case: mux split across multiple lanes. make lanes a list
# and add in extra lanes if needed.
k = mu.mux_dir
mu_dict = dict(mu._asdict())
user_data['units'][k] = mu_dict
# create mongodb update command, used later, after submission
mongo_update_cmd = "{} -r {} -s STARTED".format(mongo_status_script, user_data['run_num'])
mongo_update_cmd += " -a $ANALYSIS_ID -o {}".format(outdir)# set in run.sh
if args.testing:
mongo_update_cmd += " -t"
pipeline_handler = PipelineHandler(
PIPELINE_NAME, PIPELINE_BASEDIR,
outdir, user_data,
logger_cmd=mongo_update_cmd,
master_q=args.master_q,
slave_q=args.slave_q,
modules_cfgfile=args.modules_cfg,
cluster_cfgfile=get_cluster_cfgfile(CFG_DIR))
pipeline_handler.setup_env()
pipeline_handler.submit(args.no_run)