コード例 #1
0
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)
コード例 #2
0
ファイル: main.py プロジェクト: dlorson/bcbio-nextgen 
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)
コード例 #3
0
ファイル: main.py プロジェクト: chapmanb/bcbio-nextgen 
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)
コード例 #4
0
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)
コード例 #5
0
ファイル: multitasks.py プロジェクト: rndw/bcbio-nextgen 
def prep_system(*args):
    return run_info.prep_system(*args)
コード例 #6
0
def prep_system(*args):
    return run_info.prep_system(*args)
コード例 #7
0
ファイル: main.py プロジェクト: Cyberbio-Lab/bcbio-nextgen 
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)