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)
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)
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)
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)