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194 | usage: calrissian [-h] [--basedir BASEDIR] [--outdir OUTDIR] [--log-dir LOG_DIR] [--parallel]
[--preserve-environment ENVVAR | --preserve-entire-environment] [--rm-container | --leave-container] [--cidfile-dir CIDFILE_DIR]
[--cidfile-prefix CIDFILE_PREFIX] [--tmpdir-prefix TMPDIR_PREFIX] [--tmp-outdir-prefix TMP_OUTDIR_PREFIX | --cachedir CACHEDIR]
[--rm-tmpdir | --leave-tmpdir] [--move-outputs | --leave-outputs | --copy-outputs] [--enable-pull | --disable-pull]
[--rdf-serializer RDF_SERIALIZER] [--eval-timeout EVAL_TIMEOUT] [--provenance PROVENANCE] [--enable-user-provenance]
[--disable-user-provenance] [--enable-host-provenance] [--disable-host-provenance] [--orcid ORCID] [--full-name CWL_FULL_NAME]
[--print-rdf | --print-dot | --print-pre | --print-deps | --print-input-deps | --pack | --version | --validate | --print-supported-versions | --print-subgraph | --print-targets | --make-template]
[--strict | --non-strict] [--skip-schemas] [--no-doc-cache | --doc-cache] [--verbose | --quiet | --debug]
[--write-summary WRITE_SUMMARY] [--strict-memory-limit] [--strict-cpu-limit] [--timestamps] [--js-console] [--disable-js-validation]
[--js-hint-options-file JS_HINT_OPTIONS_FILE] [--user-space-docker-cmd CMD | --udocker | --singularity | --podman | --no-container]
[--beta-dependency-resolvers-configuration BETA_DEPENDENCY_RESOLVERS_CONFIGURATION]
[--beta-dependencies-directory BETA_DEPENDENCIES_DIRECTORY] [--beta-use-biocontainers] [--beta-conda-dependencies] [--tool-help]
[--relative-deps {primary,cwd}] [--enable-dev] [--enable-ext] [--enable-color | --disable-color]
[--default-container DEFAULT_CONTAINER] [--no-match-user] [--custom-net CUSTOM_NET]
[--enable-ga4gh-tool-registry | --disable-ga4gh-tool-registry] [--add-ga4gh-tool-registry GA4GH_TOOL_REGISTRIES]
[--on-error {stop,continue}] [--compute-checksum | --no-compute-checksum] [--relax-path-checks] [--force-docker-pull]
[--no-read-only] [--overrides OVERRIDES] [--target TARGET | --single-step SINGLE_STEP | --single-process SINGLE_PROCESS]
[--mpi-config-file MPI_CONFIG_FILE] [--max-ram MAX_RAM] [--max-cores MAX_CORES] [--pod-labels [POD_LABELS]]
[--pod-env-vars [POD_ENV_VARS]] [--pod-nodeselectors [POD_NODESELECTORS]] [--pod-serviceaccount POD_SERVICEACCOUNT]
[--usage-report [USAGE_REPORT]] [--stdout [STDOUT]] [--stderr [STDERR]] [--tool-logs-basepath [TOOL_LOGS_BASEPATH]] [--conf CONF]
[cwl_document] ...
Reference executor for Common Workflow Language standards. Not for production use.
positional arguments:
cwl_document path or URL to a CWL Workflow, CommandLineTool, or ExpressionTool. If the `inputs_object` has a `cwl:tool` field indicating
the path or URL to the cwl_document, then the `cwl_document` argument is optional.
inputs_object path or URL to a YAML or JSON formatted description of the required input values for the given `cwl_document`.
optional arguments:
-h, --help show this help message and exit
--basedir BASEDIR
--outdir OUTDIR Output directory. The default is the current directory.
--log-dir LOG_DIR Log your tools stdout/stderr to this location outside of container This will only log stdout/stderr if you specify
stdout/stderr in their respective fields or capture it as an output
--parallel [experimental] Run jobs in parallel.
--preserve-environment ENVVAR
Preserve specific environment variable when running CommandLineTools. May be provided multiple times. By default PATH is
preserved when not running in a container.
--preserve-entire-environment
Preserve all environment variables when running CommandLineTools without a software container.
--rm-container Delete Docker container used by jobs after they exit (default)
--leave-container Do not delete Docker container used by jobs after they exit
--tmpdir-prefix TMPDIR_PREFIX
Path prefix for temporary directories. If --tmpdir-prefix is not provided, then the prefix for temporary directories is
influenced by the value of the TMPDIR, TEMP, or TMP environment variables. Taking those into consideration, the current
default is /tmp/.
--tmp-outdir-prefix TMP_OUTDIR_PREFIX
Path prefix for intermediate output directories. Defaults to the value of --tmpdir-prefix.
--cachedir CACHEDIR Directory to cache intermediate workflow outputs to avoid recomputing steps. Can be very helpful in the development and
troubleshooting of CWL documents.
--rm-tmpdir Delete intermediate temporary directories (default)
--leave-tmpdir Do not delete intermediate temporary directories
--move-outputs Move output files to the workflow output directory and delete intermediate output directories (default).
--leave-outputs Leave output files in intermediate output directories.
--copy-outputs Copy output files to the workflow output directory and don't delete intermediate output directories.
--enable-pull Try to pull Docker images
--disable-pull Do not try to pull Docker images
--rdf-serializer RDF_SERIALIZER
Output RDF serialization format used by --print-rdf (one of turtle (default), n3, nt, xml)
--eval-timeout EVAL_TIMEOUT
Time to wait for a Javascript expression to evaluate before giving an error, default 60s.
--print-rdf Print corresponding RDF graph for workflow and exit
--print-dot Print workflow visualization in graphviz format and exit
--print-pre Print CWL document after preprocessing.
--print-deps Print CWL document dependencies.
--print-input-deps Print input object document dependencies.
--pack Combine components into single document and print.
--version Print version and exit
--validate Validate CWL document only.
--print-supported-versions
Print supported CWL specs.
--print-subgraph Print workflow subgraph that will execute. Can combined with --target or --single-step
--print-targets Print targets (output parameters)
--make-template Generate a template input object
--strict Strict validation (unrecognized or out of place fields are error)
--non-strict Lenient validation (ignore unrecognized fields)
--skip-schemas Skip loading of schemas
--no-doc-cache Disable disk cache for documents loaded over HTTP
--doc-cache Enable disk cache for documents loaded over HTTP
--verbose Default logging
--quiet Only print warnings and errors.
--debug Print even more logging
--write-summary WRITE_SUMMARY, -w WRITE_SUMMARY
Path to write the final output JSON object to. Default is stdout.
--strict-memory-limit
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.
--strict-cpu-limit 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.
--timestamps Add timestamps to the errors, warnings, and notifications.
--js-console Enable javascript console output
--disable-js-validation
Disable javascript validation.
--js-hint-options-file JS_HINT_OPTIONS_FILE
File of options to pass to jshint. This includes the added option "includewarnings".
--user-space-docker-cmd CMD
(Linux/OS X only) Specify the path to udocker. Implies --udocker
--udocker (Linux/OS X only) Use the udocker runtime for running containers (equivalent to --user-space-docker-cmd=udocker).
--singularity [experimental] Use Singularity runtime for running containers. Requires Singularity v2.6.1+ and Linux with kernel version
v3.18+ or with overlayfs support backported.
--podman [experimental] Use Podman runtime for running containers.
--no-container Do not execute jobs in a Docker container, even when `DockerRequirement` is specified under `hints`.
--beta-dependency-resolvers-configuration BETA_DEPENDENCY_RESOLVERS_CONFIGURATION
Dependency resolver configuration file describing how to adapt 'SoftwareRequirement' packages to current system.
--beta-dependencies-directory BETA_DEPENDENCIES_DIRECTORY
Default root directory used by dependency resolvers configuration.
--beta-use-biocontainers
Use biocontainers for tools without an explicitly annotated Docker container.
--beta-conda-dependencies
Short cut to use Conda to resolve 'SoftwareRequirement' packages.
--tool-help Print command line help for tool
--relative-deps {primary,cwd}
When using --print-deps, print paths relative to primary file or current working directory.
--enable-dev Enable loading and running unofficial development versions of the CWL standards.
--enable-ext Enable loading and running 'cwltool:' extensions to the CWL standards.
--enable-color Enable logging color (default enabled)
--disable-color Disable colored logging (default false)
--default-container DEFAULT_CONTAINER
Specify a default software container to use for any CommandLineTool without a DockerRequirement.
--no-match-user Disable passing the current uid to `docker run --user`
--custom-net CUSTOM_NET
Passed to `docker run` as the '--net' parameter when NetworkAccess is true, which is its default setting.
--enable-ga4gh-tool-registry
Enable tool resolution using GA4GH tool registry API
--disable-ga4gh-tool-registry
Disable tool resolution using GA4GH tool registry API
--add-ga4gh-tool-registry GA4GH_TOOL_REGISTRIES
Add a GA4GH tool registry endpoint to use for resolution, default ['https://dockstore.org/api']
--on-error {stop,continue}
Desired workflow behavior when a step fails. One of 'stop' (do not submit any more steps) or 'continue' (may submit other
steps that are not downstream from the error). Default is 'stop'.
--compute-checksum Compute checksum of contents while collecting outputs
--no-compute-checksum
Do not compute checksum of contents while collecting outputs
--relax-path-checks Relax requirements on path names to permit spaces and hash characters.
--force-docker-pull Pull latest software container image even if it is locally present
--no-read-only Do not set root directory in the container as read-only
--overrides OVERRIDES
Read process requirement overrides from file.
--target TARGET, -t TARGET
Only execute steps that contribute to listed targets (can be provided more than once).
--single-step SINGLE_STEP
Only executes a single step in a workflow. The input object must match that step's inputs. Can be combined with --print-
subgraph.
--single-process SINGLE_PROCESS
Only executes the underlying Process (CommandLineTool, ExpressionTool, or sub-Workflow) for the given step in a workflow. This
will not include any step-level processing: 'scatter', 'when'; and there will be no processing of step-level 'default', or
'valueFrom' input modifiers. However, requirements/hints from the step or parent workflow(s) will be inherited as usual.The
input object must match that Process's inputs.
--mpi-config-file MPI_CONFIG_FILE
Platform specific configuration for MPI (parallel launcher, its flag etc). See README section 'Running MPI-based tools' for
details of the format.
--max-ram MAX_RAM Maximum amount of RAM to use, e.g 1048576, 512Mi or 2G. Follows k8s resource conventions
--max-cores MAX_CORES
Maximum number of CPU cores to use
--pod-labels [POD_LABELS]
YAML file of labels to add to Pods submitted
--pod-env-vars [POD_ENV_VARS]
YAML file of environment variables to add at runtime to Pods submitted
--pod-nodeselectors [POD_NODESELECTORS]
YAML file of node selectors to add to Pods submitted
--pod-serviceaccount POD_SERVICEACCOUNT
Service Account to use for pods management
--usage-report [USAGE_REPORT]
Output JSON file name to record resource usage
--stdout [STDOUT] Output file name to tee standard output (CWL output object)
--stderr [STDERR] Output file name to tee standard error to (includes tool logs)
--tool-logs-basepath [TOOL_LOGS_BASEPATH]
Base path for saving the tool logs
--conf CONF Defines the default values for the CLI arguments
Options for recording the Docker container identifier into a file.:
--cidfile-dir CIDFILE_DIR
Store the Docker container ID into a file in the specified directory.
--cidfile-prefix CIDFILE_PREFIX
Specify a prefix to the container ID filename. Final file name will be followed by a timestamp. The default is no prefix.
Options for recording provenance information of the execution:
--provenance PROVENANCE
Save provenance to specified folder as a Research Object that captures and aggregates workflow execution and data products.
--enable-user-provenance
Record user account info as part of provenance.
--disable-user-provenance
Do not record user account info in provenance.
--enable-host-provenance
Record host info as part of provenance.
--disable-host-provenance
Do not record host info in provenance.
--orcid ORCID 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.
--full-name CWL_FULL_NAME
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.
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