def run(args): """Run a CWL preparation pipeline. """ dirs, config, run_info_yaml = run_info.prep_system(args.sample_config, args.systemconfig) world = run_info.organize(dirs, config, run_info_yaml) create.from_world(world, run_info_yaml)
def run(args): """Run a CWL preparation pipeline. """ dirs, config, run_info_yaml = run_info.prep_system(args.sample_config, args.systemconfig) integrations = args.integrations if hasattr(args, "integrations") else {} world = run_info.organize(dirs, config, run_info_yaml, add_provenance=False, integrations=integrations) create.from_world(world, run_info_yaml)
def run(args): """Run a CWL preparation pipeline. """ dirs, config, run_info_yaml = run_info.prep_system(args.sample_config, args.systemconfig) integrations = args.integrations if hasattr(args, "integrations") else {} world = run_info.organize(dirs, config, run_info_yaml, is_cwl=True, integrations=integrations) create.from_world(world, run_info_yaml, integrations=integrations, add_container_tag=args.add_container_tag)
def run(args): """Run a CWL preparation pipeline. """ dirs, config, run_info_yaml = run_info.prep_system(args.sample_config, args.systemconfig) integrations = args.integrations if hasattr(args, "integrations") else {} world = run_info.organize(dirs, config, run_info_yaml, add_provenance=False, integrations=integrations) create.from_world(world, run_info_yaml, integrations=integrations)
def prep_system(*args): return run_info.prep_system(*args)
def run(args): """Run a CWL preparation pipeline. """ dirs, config, run_info_yaml = run_info.prep_system(args.sample_config, args.systemconfig) world = run_info.organize(dirs, config, run_info_yaml, add_provenance=False) create.from_world(world, run_info_yaml)