def run(global_config, sample_config):
sorted_libraries_by_insert = common._sort_libraries_by_insert(sample_config)
if "tools" in sample_config:
"""If so, execute them one after the other in the specified order (might not work)"""
for command in sample_config["tools"]:
"""with this I pick up at run time the correct function in the current module"""
command_fn = getattr(sys.modules[__name__] , "_run_{}".format(command))
"""Update sample config, each command return sample_config and if necessary it modifies it"""
sample_config = command_fn(global_config, sample_config, sorted_libraries_by_insert)
else:
#run default pipeline for QC
sample_config = _run_fastqc(global_config, sample_config, sorted_libraries_by_insert)
sample_config = _run_abyss(global_config, sample_config, sorted_libraries_by_insert)
sample_config = _run_trimmomatic(global_config, sample_config, sorted_libraries_by_insert)
_run_report(global_config, sample_config,sorted_libraries_by_insert)
def run(global_config, sample_config):
sorted_libraries_by_insert = common._sort_libraries_by_insert(sample_config)
_check_libraries(sorted_libraries_by_insert)
sample_config = _build_new_reference(sample_config) # filter out short contigs
if "tools" in sample_config:
"""If so, execute them one after the other in the specified order (might not work)"""
for command in sample_config["tools"]:
"""with this I pick up at run time the correct function in the current module"""
command_fn = getattr(sys.modules[__name__] , "_run_{}".format(command))
"""Update sample config, each command return sample_config and if necessary it modifies it"""
sample_config = command_fn(global_config, sample_config, sorted_libraries_by_insert)
else:
#run default pipeline for QC
sample_config = _run_align(global_config, sample_config, sorted_libraries_by_insert)
sample_config = _run_qaTools(global_config, sample_config, sorted_libraries_by_insert)
sample_config = _run_FRC(global_config, sample_config, sorted_libraries_by_insert)
def run(global_config, sample_config):
sorted_libraries_by_insert = common._sort_libraries_by_insert(
sample_config)
if "tools" in sample_config:
"""If so, execute them one after the other in the specified order (might not work)"""
for command in sample_config["tools"]:
"""with this I pick up at run time the correct function in the current module"""
command_fn = getattr(sys.modules[__name__],
"_run_{}".format(command))
"""Update sample config, each command return sample_config and if necessary it modifies it"""
sample_config = command_fn(global_config, sample_config,
sorted_libraries_by_insert)
else:
#run default pipeline for QC
sample_config = _run_fastqc(global_config, sample_config,
sorted_libraries_by_insert)
sample_config = _run_abyss(global_config, sample_config,
sorted_libraries_by_insert)
sample_config = _run_trimmomatic(global_config, sample_config,
sorted_libraries_by_insert)
_run_report(global_config, sample_config, sorted_libraries_by_insert)
def run(global_config, sample_config):
sorted_libraries_by_insert = common._sort_libraries_by_insert(
sample_config)
_check_libraries(sorted_libraries_by_insert)
sample_config = _build_new_reference(
sample_config) # filter out short contigs
if "tools" in sample_config:
"""If so, execute them one after the other in the specified order (might not work)"""
for command in sample_config["tools"]:
"""with this I pick up at run time the correct function in the current module"""
command_fn = getattr(sys.modules[__name__],
"_run_{}".format(command))
"""Update sample config, each command return sample_config and if necessary it modifies it"""
sample_config = command_fn(global_config, sample_config,
sorted_libraries_by_insert)
else:
#run default pipeline for QC
sample_config = _run_align(global_config, sample_config,
sorted_libraries_by_insert)
sample_config = _run_qaTools(global_config, sample_config,
sorted_libraries_by_insert)
sample_config = _run_FRC(global_config, sample_config,
sorted_libraries_by_insert)
