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CWLTOOL(1) User Commands CWLTOOL(1)


cwltool - Refefence executor for Common Workflow Language


usage: cwltool [-h] [--basedir BASEDIR] [--outdir OUTDIR] [--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] [--print-rdf | --print-dot | --print-pre | --print-deps | --print-input-deps | --pack | --version | --validate | --print-supported-versions | --print-subgraph | --print-targets] [--strict | --non-strict] [--skip-schemas] [--verbose | --quiet | --debug] [--strict-memory-limit] [--timestamps] [--js-console] [--user-space-docker-cmd CMD | --singularity | --no-container] [--tool-help] [--relative-deps {primary,cwd}] [--enable-dev] [--enable-ext] [--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] [--make-template] [--force-docker-pull] [--no-read-only] [--overrides OVERRIDES] [--target TARGET] [cwl_document] ...

Reference executor for Common Workflow Language standards.

positional arguments:

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 `workflow` argument is optional.
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, default current directory
[experimental] Run jobs in parallel.
--preserve-environment ENVVAR
Preserve specific environment variable when running CommandLineTools. May be provided multiple times.
Preserve all environment variable when running CommandLineTools.
Delete Docker container used by jobs after they exit (default)
Do not delete Docker container used by jobs after they exit
--tmpdir-prefix TMPDIR_PREFIX
Path prefix for temporary directories
--tmp-outdir-prefix TMP_OUTDIR_PREFIX
Path prefix for intermediate output directories
--cachedir CACHEDIR
Directory to cache intermediate workflow outputs to avoid recomputing steps.
Delete intermediate temporary directories (default)
Do not delete intermediate temporary directories
Move output files to the workflow output directory and delete intermediate output directories (default).
Leave output files in intermediate output directories.
Copy output files to the workflow output directory, don't delete intermediate output directories.
Try to pull Docker images
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 20s.
Print corresponding RDF graph for workflow and exit
Print workflow visualization in graphviz format and exit
Print CWL document after preprocessing.
Print CWL document dependencies.
Print input object document dependencies.
Combine components into single document and print.
Print version and exit
Validate CWL document only.
Print supported CWL specs.
Print workflow subgraph that will execute (can combine with --target)
Print targets (output parameters)
Strict validation (unrecognized or out of place fields are error)
Lenient validation (ignore unrecognized fields)
Skip loading of schemas
Default logging
Only print warnings and errors.
Print even more logging
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.
Add timestamps to the errors, warnings, and notifications.
Enable javascript console output
--user-space-docker-cmd CMD
(Linux/OS X only) Specify a user space docker command (like udocker or dx-docker) that will be used to call 'pull' and 'run'
[experimental] Use Singularity runtime for running containers. Requires Singularity v2.3.2+ and Linux with kernel version v3.18+ or with overlayfs support backported.
Do not execute jobs in a Docker container, even when `DockerRequirement` is specified under `hints`.
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 loading and running development versions of CWL spec.
Enable loading and running cwltool extensions to CWL spec.
--default-container DEFAULT_CONTAINER
Specify a default docker container that will be used if the workflow fails to specify one.
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.
Enable resolution using GA4GH tool registry API
Disable resolution using GA4GH tool registry API
--add-ga4gh-tool-registry GA4GH_TOOL_REGISTRIES
Add a GA4GH tool registry endpoint to use for resolution, default ['']
--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 of contents while collecting outputs
Do not compute checksum of contents while collecting outputs
Relax requirements on path names to permit spaces and hash characters.
Generate a template input object
Pull latest docker image even if it is locally present
Do not set root directory in the container as readonly
--overrides OVERRIDES
Read process requirement overrides from file.
--target TARGET, -t TARGET
Only execute steps that contribute to listed targets (can provide more than once).

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.

January 2019 cwltool 1.0.20181217162649+dfsg