def test_bcbb_command(self):
"""Test output from command, changing analysis to amplicon and
setting targets and baits"""
flist = find_samples(j_doe_00_05)
for f in flist:
setup_sample(f, **{'analysis':ANALYSIS_TYPE, 'genome_build':'rn4', 'dry_run':False,
'no_only_run':False, 'google_report':False,
'dry_run':False, 'baits':'rat_baits.interval_list', 'targets':'rat_targets.interval_list', 'amplicon':True, 'num_cores':8, 'distributed':False})
with open(f.replace("-bcbb-config.yaml", "-bcbb-command.txt")) as fh:
cl = fh.read().split()
(cl, platform_args) = run_bcbb_command(f)
self.assertIn("automated_initial_analysis.py",cl)
setup_sample(f, **{'analysis':ANALYSIS_TYPE, 'genome_build':'rn4', 'dry_run':False,
'no_only_run':False, 'google_report':False,
'dry_run':False, 'baits':'rat_baits.interval_list', 'targets':'rat_targets.interval_list', 'amplicon':True, 'num_cores':8, 'distributed':True})
with open(f.replace("-bcbb-config.yaml", "-bcbb-command.txt")) as fh:
cl = fh.read().split()
(cl, platform_args) = run_bcbb_command(f)
self.assertIn("distributed_nextgen_pipeline.py",cl)
def test_bcbb_command(self):
"""Test output from command, changing analysis to amplicon and
setting targets and baits"""
flist = find_samples(j_doe_00_05)
for f in flist:
setup_sample(
f, **{
'analysis': ANALYSIS_TYPE,
'genome_build': 'rn4',
'dry_run': False,
'no_only_run': False,
'google_report': False,
'dry_run': False,
'baits': 'rat_baits.interval_list',
'targets': 'rat_targets.interval_list',
'amplicon': True,
'num_cores': 8,
'distributed': False
})
with open(f.replace("-bcbb-config.yaml",
"-bcbb-command.txt")) as fh:
cl = fh.read().split()
(cl, platform_args) = run_bcbb_command(f)
self.assertIn("automated_initial_analysis.py", cl)
setup_sample(
f, **{
'analysis': ANALYSIS_TYPE,
'genome_build': 'rn4',
'dry_run': False,
'no_only_run': False,
'google_report': False,
'dry_run': False,
'baits': 'rat_baits.interval_list',
'targets': 'rat_targets.interval_list',
'amplicon': True,
'num_cores': 8,
'distributed': True
})
with open(f.replace("-bcbb-config.yaml",
"-bcbb-command.txt")) as fh:
cl = fh.read().split()
(cl, platform_args) = run_bcbb_command(f)
self.assertIn("distributed_nextgen_pipeline.py", cl)
def run(self):
if not self._check_pargs(["project"]):
return
if self.pargs.post_process:
self.pargs.post_process = os.path.abspath(self.pargs.post_process)
basedir = os.path.abspath(os.path.join(self.app.controller._meta.root_path, self.app.controller._meta.path_id))
if self.pargs.from_ssheet:
[
samplesheet_csv_to_yaml(fn)
for fn in find_samples(basedir, pattern="SampleSheet.csv$", **vars(self.pargs))
]
flist = find_samples(basedir, **vars(self.pargs))
# Add filtering on flowcell if necessary
self._meta.pattern = ".*"
flist = [x for x in flist if self._filter_fn(x)]
if self.pargs.merged:
## Setup merged samples and append to flist if new list longer
flist = setup_merged_samples(flist, **vars(self.pargs))
if not len(flist) > 0:
self.log.info("No sample configuration files found")
return
if len(flist) > 0 and not query_yes_no(
"Going to start {} jobs... Are you sure you want to continue?".format(len(flist)), force=self.pargs.force
):
return
# Make absolutely sure analysis directory is a *subdirectory* of the working directory
validate_sample_directories(flist, basedir)
orig_dir = os.path.abspath(os.getcwd())
for run_info in flist:
os.chdir(os.path.abspath(os.path.dirname(run_info)))
setup_sample(run_info, **vars(self.pargs))
os.chdir(orig_dir)
if self.pargs.only_setup:
return
if self.pargs.only_failed:
status = {x: self._sample_status(x) for x in flist}
flist = [x for x in flist if self._sample_status(x) == "FAIL"]
## Here process files again, removing if requested, and running the pipeline
for run_info in flist:
self.app.log.info("Running analysis defined by config file {}".format(run_info))
os.chdir(os.path.abspath(os.path.dirname(run_info)))
if self.app.cmd.monitor(work_dir=os.path.dirname(run_info)):
self.app.log.warn("Not running job")
continue
if self.pargs.restart:
self.app.log.info("Removing old analysis files in {}".format(os.path.dirname(run_info)))
remove_files(run_info, **vars(self.pargs))
(cl, platform_args) = run_bcbb_command(run_info, **vars(self.pargs))
self.app.cmd.command(
cl, **{"platform_args": platform_args, "saveJobId": True, "workingDirectory": os.path.dirname(run_info)}
)
os.chdir(orig_dir)
def test_global_post_process(self):
"""Test that when using a "global" post_process, jobname,
output, error and output directory are updated.
"""
flist = find_samples(j_doe_00_05)
pp = os.path.join(j_doe_00_01, SAMPLES[1], FLOWCELL, "{}-post_process.yaml".format(SAMPLES[1]))
with open(pp) as fh:
postprocess = yaml.load(fh)
for f in flist:
(cl, platform_args) = run_bcbb_command(f, pp)
self.assertIn("--error", platform_args)
self.assertEqual(platform_args[platform_args.index("--error") + 1], f.replace("-bcbb-config.yaml", "-bcbb.err"))
def test_global_post_process(self):
"""Test that when using a "global" post_process, jobname,
output, error and output directory are updated.
"""
flist = find_samples(j_doe_00_05)
pp = os.path.join(j_doe_00_01, SAMPLES[1], FLOWCELL,
"{}-post_process.yaml".format(SAMPLES[1]))
with open(pp) as fh:
postprocess = yaml.load(fh)
for f in flist:
(cl, platform_args) = run_bcbb_command(f, pp)
self.assertIn("--error", platform_args)
self.assertEqual(platform_args[platform_args.index("--error") + 1],
f.replace("-bcbb-config.yaml", "-bcbb.err"))
def run(self):
if not self._check_pargs(["project"]):
return
if self.pargs.post_process:
self.pargs.post_process = os.path.abspath(self.pargs.post_process)
basedir = os.path.abspath(
os.path.join(self.app.controller._meta.root_path,
self.app.controller._meta.path_id))
if self.pargs.from_ssheet:
[
samplesheet_csv_to_yaml(fn) for fn in find_samples(
basedir, pattern="SampleSheet.csv$", **vars(self.pargs))
]
flist = find_samples(basedir, **vars(self.pargs))
# Add filtering on flowcell if necessary
self._meta.pattern = ".*"
flist = [x for x in flist if self._filter_fn(x)]
if self.pargs.merged:
## Setup merged samples and append to flist if new list longer
flist = setup_merged_samples(flist, **vars(self.pargs))
if not len(flist) > 0:
self.log.info("No sample configuration files found")
return
if len(flist) > 0 and not query_yes_no(
"Going to start {} jobs... Are you sure you want to continue?".
format(len(flist)),
force=self.pargs.force):
return
# Make absolutely sure analysis directory is a *subdirectory* of the working directory
validate_sample_directories(flist, basedir)
orig_dir = os.path.abspath(os.getcwd())
for run_info in flist:
os.chdir(os.path.abspath(os.path.dirname(run_info)))
setup_sample(run_info, **vars(self.pargs))
os.chdir(orig_dir)
if self.pargs.only_setup:
return
if self.pargs.only_failed:
status = {x: self._sample_status(x) for x in flist}
flist = [x for x in flist if self._sample_status(x) == "FAIL"]
## Here process files again, removing if requested, and running the pipeline
for run_info in flist:
self.app.log.info(
"Running analysis defined by config file {}".format(run_info))
os.chdir(os.path.abspath(os.path.dirname(run_info)))
if self.app.cmd.monitor(work_dir=os.path.dirname(run_info)):
self.app.log.warn("Not running job")
continue
if self.pargs.restart:
self.app.log.info("Removing old analysis files in {}".format(
os.path.dirname(run_info)))
remove_files(run_info, **vars(self.pargs))
(cl, platform_args) = run_bcbb_command(run_info,
**vars(self.pargs))
self.app.cmd.command(
cl, **{
'platform_args': platform_args,
'saveJobId': True,
'workingDirectory': os.path.dirname(run_info)
})
os.chdir(orig_dir)