cwltool Command Line Options

cwltool

Reference executor for Common Workflow Language standards. Not for production use.

usage: cwltool [-h] [--basedir BASEDIR] [--outdir OUTDIR]
               [--write-summary WRITE_SUMMARY] [--parallel]
               [--parallel-max PARALLEL_MAX] [--skip-schemas] [--enable-dev]
               [--enable-ext] [--on-error {stop,continue}]
               [--relax-path-checks] [--overrides OVERRIDES]
               [--mpi-config-file MPI_CONFIG_FILE] [--print-rdf |
               --print-dot | --print-pre | --print-deps | --print-input-deps |
               --pack | --version | --validate | --print-supported-versions |
               --print-subgraph | --print-targets | --make-template]
               [--relative-deps {primary,cwd}]
               [--rdf-serializer RDF_SERIALIZER] [--tool-help] [--verbose |
               --no-warnings | --quiet | --debug] [--log-dir LOG_DIR]
               [--timestamps] [--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] [--strict | --non-strict]
               [--no-doc-cache | --doc-cache] [--user-space-docker-cmd CMD |
               --udocker | --singularity | --podman | --no-container]
               [--enable-pull | --disable-pull]
               [--singularity-sandbox-path IMAGE_BASE_PATH]
               [--force-docker-pull] [--no-read-only]
               [--default-container DEFAULT_CONTAINER] [--no-match-user]
               [--custom-net CUSTOM_NET] [--strict-memory-limit]
               [--strict-cpu-limit] [--rm-container | --leave-container]
               [--cidfile-dir CIDFILE_DIR] [--cidfile-prefix CIDFILE_PREFIX]
               [--beta-dependency-resolvers-configuration BETA_DEPENDENCY_RESOLVERS_CONFIGURATION]
               [--beta-dependencies-directory BETA_DEPENDENCIES_DIRECTORY]
               [--beta-use-biocontainers] [--beta-conda-dependencies]
               [--enable-color | --disable-color]
               [--enable-ga4gh-tool-registry | --disable-ga4gh-tool-registry]
               [--add-ga4gh-tool-registry GA4GH_TOOL_REGISTRIES]
               [--compute-checksum | --no-compute-checksum]
               [--eval-timeout EVAL_TIMEOUT] [--js-console]
               [--disable-js-validation]
               [--js-hint-options-file JS_HINT_OPTIONS_FILE]
               [--target TARGET | --single-step SINGLE_STEP |
               --single-process SINGLE_PROCESS]
               [cwl_document] ...

environment variables

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

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 <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.

dependency resolver configuration

--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 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 <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.