Ubuntu Manpage: cwltool - Refefence executor for Common Workflow Language

Provided by: cwltool_3.1.20250110105449-3_all

NAME

       cwltool - Refefence executor for Common Workflow Language

DESCRIPTION

usage: cwltool [-h] [--basedir BASEDIR] [--outdir OUTDIR] [--parallel]

[--preserve-environment ENVVAR | --preserve-entire-environment] [--tmpdir-prefix TMPDIR_PREFIX]
[--tmp-outdir-prefix TMP_OUTDIR_PREFIX | --cachedir CACHEDIR] [--rm-tmpdir | --leave-tmpdir]
[--move-outputs | --leave-outputs | --copy-outputs] [--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 | --make-template]
[--rdf-serializer RDF_SERIALIZER] [--tool-help] [--strict | --non-strict] [--skip-schemas]
[--no-doc-cache | --doc-cache] [--verbose | --no-warnings | --quiet | --debug] [--log-dir LOG_DIR]
[--timestamps] [--write-summary WRITE_SUMMARY] [--js-console] [--disable-js-validation]
[--js-hint-options-file JS_HINT_OPTIONS_FILE] [--enable-pull | --disable-pull]
[--force-docker-pull] [--no-read-only] [--default-container DEFAULT_CONTAINER] [--no-match-user]
[--custom-net CUSTOM_NET] [--rm-container | --leave-container] [--cidfile-dir CIDFILE_DIR]
[--cidfile-prefix CIDFILE_PREFIX] [--user-space-docker-cmd CMD | --udocker | --singularity |
--podman | --no-container] [--strict-memory-limit] [--strict-cpu-limit] [--relative-deps
{primary,cwd}] [--enable-dev] [--enable-ext] [--enable-color | --disable-color]
[--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] [--overrides OVERRIDES] [--target TARGET | --single-step SINGLE_STEP |
--single-process SINGLE_PROCESS] [--mpi-config-file MPI_CONFIG_FILE] [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`.

options:
-h, --help
show this help message and exit

--basedir BASEDIR

--outdir OUTDIR
Output directory. The default is the current directory.

--parallel
Run jobs in parallel.

--eval-timeout EVAL_TIMEOUT
Time to wait for a Javascript expression to evaluate before giving an error, default 60s.

--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

--write-summary, -w WRITE_SUMMARY
Path to write the final output JSON object to. Default is stdout.

--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".

--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)

--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.

--overrides OVERRIDES
Read process requirement overrides from file.

--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.

Control environment variables:
--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.

Manage intermediate, temporary, or final output files:
--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.

Non-execution options:
--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

--rdf-serializer RDF_SERIALIZER
Output RDF serialization format used by --print-rdf (one of turtle (default), n3, nt, xml)

--tool-help
Print command line help for tool

Configure logging:
--verbose
Default logging

--no-warnings
Only print errors.

--quiet
Only print warnings and errors.

--debug
Print even more logging

--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

--timestamps
Add timestamps to the errors, warnings, and notifications.

Software container engine selection and configuration:
--enable-pull
Try to pull Docker images

--disable-pull
Do not try to pull Docker images

--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

--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.

--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

--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
Use Singularity or Apptainer runtime for running containers. Requires Singularity v2.6.1+ and
Linux with kernel version v3.18+ or with overlayfs support backported.

--podman
Use Podman runtime for running containers.

--no-container
Do not execute jobs in a Docker container, even when `DockerRequirement` is specified under
`hints`.

--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.

Target selection (optional):
--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.

NAME

DESCRIPTION

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