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.

--write-summary, -w WRITE_SUMMARY

Path to write the final output JSON object to. Default is stdout.

--parallel

Run jobs in parallel.

--parallel-max PARALLEL_MAX

Maximum number of jobs to run in parallel. Specify '0' to match the number of CPU cores available.

--skip-schemas

Skip loading of schemas

--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.

--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`.

--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.

--strict

Strict validation (unrecognized or out of place fields are errors)

--non-strict

Lenient validation (ignore unrecognized fields)

--no-doc-cache

Disable disk cache for documents loaded over HTTP

--doc-cache

Enable disk cache for documents loaded over HTTP

--enable-color

Enable logging color (default enabled)

--disable-color

Disable colored logging (default false)

--compute-checksum

Compute checksum of contents while collecting outputs

--no-compute-checksum

Do not compute checksum of contents while collecting outputs

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

--relative-deps {primary,cwd}

When using --print-deps, print paths relative to primary file or current working directory.

--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

logging configuration:¶

--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.

environment variables control:¶

--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.

intermediate, temporary, or final output files management:¶

--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.

software container engine selection and configuration:¶

--user-space-docker-cmd CMD

Specify the path to udocker. Implies --udocker

--udocker

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`.

--enable-pull

Try to pull Docker images

--disable-pull

Do not try to pull Docker images

--singularity-sandbox-path IMAGE_BASE_PATH

Singularity/Apptainer sandbox image base path. Will use a pre-existing sandbox image. Will be prepended to the dockerPull path. Equivalent to use CWL_SINGULARITY_IMAGES variable.

--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.

--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.

--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

--cidfile-dir CIDFILE_DIR

Store the software container ID into a file in the specified directory.

--cidfile-prefix CIDFILE_PREFIX

Specify a prefix to the software container ID filename. Final file name will be followed by a timestamp. The default is no prefix.

tool resolution:¶

(using the GA4GH Tool Registry Service (TRS) API)

--enable-ga4gh-tool-registry

Enable tool resolution using GA4GH TRS API

--disable-ga4gh-tool-registry

Disable tool resolution using GA4GH TRS API

--add-ga4gh-tool-registry GA4GH_TOOL_REGISTRIES

Add a GA4GH TRS endpoint to use for resolution, default ['https://dockstore.org/api']

javascript options:¶

--eval-timeout EVAL_TIMEOUT

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

--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".

execution target selection:¶

(optional, by default all target contributing to final outputs are executed)

--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.

environment variable

??? usage

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CWLTOOL_OPTIONS

??? set additional space-separated cwltool options

CWL_FULL_NAME

??? full name of user to record as part of --provenance

CWL_SINGULARITY_CACHE ??? directory path to find already downloaded

??? Singularity images; dockerFile images will also be ??? searched for and stored here

ORCID

??? user ORCID identifier to record as part of ??? --provenance

XDG_CACHE_HOME

??? directory path to store cached HTTP(S) downloads in ??? a cwltool sub-folder; if unset, then cache downloads ??? are stored in $HOME/.cache/cwltool

XDG_DATA_HOME

??? directory path to search for a .local/commonwl CWL ??? tool folder; if unset, then $HOME/.local/commonwl is ??? searched

XDG_DATA_DIRS

??? directory path to search for a commonwl CWL tool ??? folder; if unset, then /usr/local/share/ and ??? /usr/share/ are searched