import os
from argparse import ArgumentParser
from configargparse import SUPPRESS
from toil.version import baseVersion
[docs]
def add_cwl_options(parser: ArgumentParser, suppress: bool = True) -> None:
"""
Add CWL options to the parser. This only adds nonpositional CWL arguments.
:param parser: Parser to add options to
:param suppress: Suppress help output
:return: None
"""
suppress_help = SUPPRESS if suppress else None
parser.add_argument("--not-strict", action="store_true", help=suppress_help)
parser.add_argument(
"--enable-dev",
action="store_true",
help=suppress_help or suppress_help or "Enable loading and running development versions of CWL",
)
parser.add_argument(
"--enable-ext",
action="store_true",
help=suppress_help or "Enable loading and running 'cwltool:' extensions to the CWL standards.",
default=False,
)
parser.add_argument("--quiet", dest="quiet", action="store_true", default=False, help=suppress_help)
parser.add_argument("--basedir", type=str, help=suppress_help) # TODO: Might be hard-coded?
parser.add_argument("--outdir", type=str, default=None, help=suppress_help)
parser.add_argument("--version", action="version", version=baseVersion,
help=suppress_help or "show program's version number and exit")
parser.add_argument(
"--log-dir",
type=str,
default="",
help=suppress_help or "Log your tools stdout/stderr to this location outside of container",
)
# this is as a result of suppressed help statements not working well with mutually_exclusive_groups, which will
# cause an assertion error
# https://github.com/python/cpython/issues/62090
dockergroup = parser.add_mutually_exclusive_group() if not suppress_help else parser.add_argument_group()
dockergroup.add_argument(
"--user-space-docker-cmd",
help=suppress_help or "(Linux/OS X only) Specify a user space docker command (like "
"udocker or dx-docker) that will be used to call 'pull' and 'run'",
)
dockergroup.add_argument(
"--singularity",
action="store_true",
default=False,
help=suppress_help or "Use Singularity runtime for running containers. "
"Requires Singularity v2.6.1+ and Linux with kernel version v3.18+ or "
"with overlayfs support backported.",
)
dockergroup.add_argument(
"--podman",
action="store_true",
default=False,
help=suppress_help or "Use Podman runtime for running containers. ",
)
dockergroup.add_argument(
"--no-container",
action="store_true",
help=suppress_help or "Do not execute jobs in a "
"Docker container, even when `DockerRequirement` "
"is specified under `hints`.",
)
dockergroup.add_argument(
"--leave-container",
action="store_false",
default=True,
help=suppress_help or "Do not delete Docker container used by jobs after they exit",
dest="rm_container",
)
extra_dockergroup = parser.add_argument_group()
extra_dockergroup.add_argument(
"--custom-net",
help=suppress_help or "Specify docker network name to pass to docker run command",
)
cidgroup = parser.add_argument_group(
"Options for recording the Docker container identifier into a file."
)
cidgroup.add_argument(
# Disabled as containerid is now saved by default
"--record-container-id",
action="store_true",
default=False,
help=suppress_help or SUPPRESS,
dest="record_container_id",
)
cidgroup.add_argument(
"--cidfile-dir",
type=str,
help=suppress_help or "Store the Docker container ID into a file in the specified directory.",
default=None,
dest="cidfile_dir",
)
cidgroup.add_argument(
"--cidfile-prefix",
type=str,
help=suppress_help or "Specify a prefix to the container ID filename. "
"Final file name will be followed by a timestamp. "
"The default is no prefix.",
default=None,
dest="cidfile_prefix",
)
parser.add_argument(
"--preserve-environment",
type=str,
nargs="+",
help=suppress_help or "Preserve specified environment variables when running"
" CommandLineTools",
metavar=("VAR1 VAR2"),
default=("PATH",),
dest="preserve_environment",
)
parser.add_argument(
"--preserve-entire-environment",
action="store_true",
help=suppress_help or "Preserve all environment variable when running CommandLineTools.",
default=False,
dest="preserve_entire_environment",
)
parser.add_argument(
"--destBucket",
type=str,
help=suppress_help or "Specify a cloud bucket endpoint for output files.",
)
parser.add_argument("--beta-dependency-resolvers-configuration", default=None, help=suppress_help)
parser.add_argument("--beta-dependencies-directory", default=None, help=suppress_help)
parser.add_argument("--beta-use-biocontainers", default=None, action="store_true", help=suppress_help)
parser.add_argument("--beta-conda-dependencies", default=None, action="store_true", help=suppress_help)
parser.add_argument(
"--tmpdir-prefix",
type=str,
help=suppress_help or "Path prefix for temporary directories",
default=None,
)
parser.add_argument(
"--tmp-outdir-prefix",
type=str,
help=suppress_help or "Path prefix for intermediate output directories",
default=None,
)
parser.add_argument(
"--force-docker-pull",
action="store_true",
default=False,
dest="force_docker_pull",
help=suppress_help or "Pull latest docker image even if it is locally present",
)
parser.add_argument(
"--no-match-user",
action="store_true",
default=False,
help=suppress_help or "Disable passing the current uid to `docker run --user`",
)
parser.add_argument(
"--no-read-only",
action="store_true",
default=False,
help=suppress_help or "Do not set root directory in the container as read-only",
)
parser.add_argument(
"--strict-memory-limit",
action="store_true",
help=suppress_help or "When running with "
"software containers and the Docker engine, pass either the "
"calculated memory allocation from ResourceRequirements or the "
"default of 1 gigabyte to Docker's --memory option.",
)
parser.add_argument(
"--strict-cpu-limit",
action="store_true",
help=suppress_help or "When running with "
"software containers and the Docker engine, pass either the "
"calculated cpu allocation from ResourceRequirements or the "
"default of 1 core to Docker's --cpu option. "
"Requires docker version >= v1.13.",
)
parser.add_argument(
"--relax-path-checks",
action="store_true",
default=False,
help=suppress_help or "Relax requirements on path names to permit "
"spaces and hash characters.",
dest="relax_path_checks",
)
parser.add_argument(
"--default-container",
help=suppress_help or "Specify a default docker container that will be "
"used if the workflow fails to specify one.",
)
parser.add_argument(
"--disable-validate",
dest="do_validate",
action="store_false",
default=True,
help=suppress_help or SUPPRESS,
)
parser.add_argument(
"--fast-parser",
dest="fast_parser",
action="store_true",
default=False,
help=suppress_help or SUPPRESS,
)
# same workaround as dockergroup
checkgroup = parser.add_mutually_exclusive_group() if not suppress_help else parser.add_argument_group()
checkgroup.add_argument(
"--compute-checksum",
action="store_true",
default=True,
help=suppress_help or "Compute checksum of contents while collecting outputs",
dest="compute_checksum",
)
checkgroup.add_argument(
"--no-compute-checksum",
action="store_false",
help=suppress_help or "Do not compute checksum of contents while collecting outputs",
dest="compute_checksum",
)
parser.add_argument(
"--eval-timeout",
help=suppress_help or "Time to wait for a Javascript expression to evaluate before giving "
"an error, default 20s.",
type=float,
default=20,
)
parser.add_argument(
"--overrides",
type=str,
default=None,
help=suppress_help or "Read process requirement overrides from file.",
)
parser.add_argument(
"--mpi-config-file",
type=str,
default=None,
help=suppress_help or "Platform specific configuration for MPI (parallel "
"launcher, its flag etc). See the cwltool README "
"section 'Running MPI-based tools' for details of the format: "
"https://github.com/common-workflow-language/cwltool#running-mpi-based-tools-that-need-to-be-launched",
)
parser.add_argument(
"--bypass-file-store",
action="store_true",
default=False,
help=suppress_help or "Do not use Toil's file store and assume all "
"paths are accessible in place from all nodes.",
dest="bypass_file_store",
)
parser.add_argument(
"--reference-inputs",
action="store_true",
default=False,
help=suppress_help or "Do not copy remote inputs into Toil's file "
"store and assume they are accessible in place from "
"all nodes.",
dest="reference_inputs",
)
parser.add_argument(
"--disable-streaming",
action="store_true",
default=False,
help=suppress_help or "Disable file streaming for files that have 'streamable' flag True",
dest="disable_streaming",
)
provgroup = parser.add_argument_group(
"Options for recording provenance information of the execution"
)
provgroup.add_argument(
"--provenance",
help=suppress_help or "Save provenance to specified folder as a "
"Research Object that captures and aggregates "
"workflow execution and data products.",
type=str,
)
provgroup.add_argument(
"--enable-user-provenance",
default=False,
action="store_true",
help=suppress_help or "Record user account info as part of provenance.",
dest="user_provenance",
)
provgroup.add_argument(
"--disable-user-provenance",
default=False,
action="store_false",
help=suppress_help or "Do not record user account info in provenance.",
dest="user_provenance",
)
provgroup.add_argument(
"--enable-host-provenance",
default=False,
action="store_true",
help=suppress_help or "Record host info as part of provenance.",
dest="host_provenance",
)
provgroup.add_argument(
"--disable-host-provenance",
default=False,
action="store_false",
help=suppress_help or "Do not record host info in provenance.",
dest="host_provenance",
)
provgroup.add_argument(
"--orcid",
help=suppress_help or "Record user ORCID identifier as part of "
"provenance, e.g. https://orcid.org/0000-0002-1825-0097 "
"or 0000-0002-1825-0097. Alternatively the environment variable "
"ORCID may be set.",
dest="orcid",
default=os.environ.get("ORCID", ""),
type=str,
)
provgroup.add_argument(
"--full-name",
help=suppress_help or "Record full name of user as part of provenance, "
"e.g. Josiah Carberry. You may need to use shell quotes to preserve "
"spaces. Alternatively the environment variable CWL_FULL_NAME may "
"be set.",
dest="cwl_full_name",
default=os.environ.get("CWL_FULL_NAME", ""),
type=str,
)
