def build(args):
welcome = [
"========= F L O W C R A F T =========",
"Build mode\n"
"version: {}".format(__version__),
"build: {}".format(__build__),
"====================================="
]
parsed_output_nf = validate_build_arguments(args)
logger.info(colored_print("\n".join(welcome), "green_bold"))
# If a recipe is specified, build pipeline based on the
# appropriate recipe
if args.recipe:
pipeline_string, list_processes = brew_recipe(args)
else:
pipeline_string = args.tasks
list_processes = None
# used for lists print
proc_collector(process_map, args, list_processes)
logger.info(colored_print("Resulting pipeline string:\n"))
logger.info(colored_print(pipeline_string + "\n"))
try:
logger.info(colored_print("Checking pipeline for errors..."))
pipeline_list = parse_pipeline(pipeline_string)
except SanityError as e:
logger.error(colored_print(e.value, "red_bold"))
sys.exit(1)
logger.debug("Pipeline successfully parsed: {}".format(pipeline_list))
# Exit if only the pipeline parser needs to be checked
if args.check_only:
sys.exit()
nfg = NextflowGenerator(process_connections=pipeline_list,
nextflow_file=parsed_output_nf,
pipeline_name=args.pipeline_name,
auto_dependency=args.no_dep)
logger.info(colored_print("Building your awesome pipeline..."))
# building the actual pipeline nf file
nfg.build()
# copy template to cwd, to allow for immediate execution
if not args.pipeline_only:
copy_project(parsed_output_nf)
logger.info(colored_print("DONE!", "green_bold"))
def build(args):
# Disable standard logging for stdout when the following modes are
# executed:
if args.export_params or args.export_directives:
logger.setLevel(logging.ERROR)
welcome = [
"========= F L O W C R A F T =========",
"Build mode\n"
"version: {}".format(__version__),
"build: {}".format(__build__),
"====================================="
]
parsed_output_nf = validate_build_arguments(args)
logger.info(colored_print("\n".join(welcome), "green_bold"))
# If a recipe is specified, build pipeline based on the
# appropriate recipe
if args.recipe:
if args.recipe == "innuendo":
pipeline_string = brew_recipe(args, available_recipes)
else:
pipeline_string = available_recipes[args.recipe]
if args.tasks:
logger.warning(colored_print(
"-t parameter will be ignored for recipe: {}\n"
.format(args.recipe), "yellow_bold")
)
if args.check_recipe:
logger.info(colored_print("Pipeline string for recipe: {}"
.format(args.recipe), "purple_bold"))
logger.info(pipeline_string)
sys.exit(0)
else:
pipeline_string = args.tasks
# used for lists print
proc_collector(process_map, args, pipeline_string)
try:
logger.info(colored_print("Checking pipeline for errors..."))
pipeline_list = parse_pipeline(pipeline_string)
except SanityError as e:
logger.error(colored_print(e.value, "red_bold"))
sys.exit(1)
logger.debug("Pipeline successfully parsed: {}".format(pipeline_list))
# Exit if only the pipeline parser needs to be checked
if args.check_only:
sys.exit()
nfg = NextflowGenerator(process_connections=pipeline_list,
nextflow_file=parsed_output_nf,
pipeline_name=args.pipeline_name,
auto_dependency=args.no_dep,
merge_params=args.merge_params,
export_params=args.export_params)
logger.info(colored_print("Building your awesome pipeline..."))
if args.export_params:
nfg.export_params()
sys.exit(0)
elif args.export_directives:
nfg.export_directives()
sys.exit(0)
else:
# building the actual pipeline nf file
nfg.build()
# copy template to cwd, to allow for immediate execution
if not args.pipeline_only:
copy_project(parsed_output_nf)
logger.info(colored_print("DONE!", "green_bold"))
def run(args):
if args.debug:
logger.setLevel(logging.DEBUG)
# create formatter
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s')
else:
logger.setLevel(logging.INFO)
# create special formatter for info logs
formatter = logging.Formatter('%(message)s')
# create console handler and set level to debug
ch = logging.StreamHandler(sys.stdout)
ch.setLevel(logging.DEBUG)
# add formatter to ch
ch.setFormatter(formatter)
logger.addHandler(ch)
welcome = [
"========= A S S E M B L E R F L O W =========",
"version: {}".format(__version__), "build: {}".format(__build__),
"============================================="
]
logger.info(colored_print("\n".join(welcome), "green_bold"))
# If a recipe is specified, build pipeline based on the
# appropriate recipe
if args.recipe:
pipeline_string, list_processes = brew_recipe(args)
else:
pipeline_string = args.tasks
list_processes = None
# used for lists print
proc_collector(process_map, args, list_processes)
# Validate arguments. This must be done after the process collector part
passed = check_arguments(args)
if not passed:
return
logger.info(colored_print("Resulting pipeline string:\n"))
logger.info(colored_print(pipeline_string + "\n"))
try:
logger.info(colored_print("Checking pipeline for errors..."))
pipeline_list = parse_pipeline(pipeline_string)
except SanityError as e:
logger.error(colored_print(e.value, "red_bold"))
sys.exit(1)
logger.debug("Pipeline successfully parsed: {}".format(pipeline_list))
# Exit if only the pipeline parser needs to be checked
if args.check_only:
sys.exit()
nfg = NextflowGenerator(process_connections=pipeline_list,
nextflow_file=args.output_nf)
logger.info(colored_print("Building your awesome pipeline..."))
# building the actual pipeline nf file
nfg.build()
# copy template to cwd, to allow for immediate execution
if args.include_templates:
copy_project(args.output_nf)
logger.info(colored_print("DONE!", "green_bold"))