예제 #1
0
def _template_cmd(subparsers):
    parser = subparsers.add_parser("template",
                                   help="Create a bcbio sample.yaml file from a standard template and inputs")
    parser = template.setup_args(parser)
    parser.add_argument('--relpaths', help="Convert inputs into relative paths to the work directory",
                        action='store_true', default=False)
    parser.set_defaults(func=template.setup)
예제 #2
0
def _template_cmd(subparsers):
    parser = subparsers.add_parser("template",
                                   help="Create a bcbio sample.yaml file from a standard template and inputs")
    parser = template.setup_args(parser)
    parser = _std_config_args(parser)
    parser.add_argument('--relpaths', help="Convert inputs into relative paths to the work directory",
                        action='store_true', default=False)
    parser.set_defaults(integrations={"arvados": arvados_retriever})
    parser.set_defaults(func=template.setup)
예제 #3
0
def _template_cmd(subparsers):
    parser = subparsers.add_parser("template",
                                   help="Create a bcbio sample.yaml file from a standard template and inputs")
    parser = template.setup_args(parser)
    parser = _std_config_args(parser)
    parser.add_argument('--relpaths', help="Convert inputs into relative paths to the work directory",
                        action='store_true', default=False)
    parser.set_defaults(integrations={"arvados": arvados_retriever, "s3": s3retriever, "sbgenomics": sb_retriever,
                                      "dnanexus": dx_retriever, "gs": gs_retriever, "local": localref})
    parser.set_defaults(func=template.setup)
예제 #4
0
def _template_cmd(subparsers):
    parser = subparsers.add_parser("template",
                                   help="Create a bcbio sample.yaml file from a standard template and inputs")
    parser = template.setup_args(parser)
    parser.set_defaults(func=template.setup)