.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH CWLTOOL "1" "January 2019" "cwltool 1.0.20181217162649+dfsg" "User Commands"
.SH NAME
cwltool - Refefence executor for Common Workflow Language
.SH DESCRIPTION
usage: cwltool [\-h] [\-\-basedir BASEDIR] [\-\-outdir OUTDIR] [\-\-parallel]
.IP
[\-\-preserve\-environment ENVVAR | \fB\-\-preserve\-entire\-environment]\fR
[\-\-rm\-container | \fB\-\-leave\-container]\fR
[\-\-cidfile\-dir CIDFILE_DIR]
[\-\-cidfile\-prefix CIDFILE_PREFIX]
[\-\-tmpdir\-prefix TMPDIR_PREFIX]
[\-\-tmp\-outdir\-prefix TMP_OUTDIR_PREFIX | \fB\-\-cachedir\fR CACHEDIR]
[\-\-rm\-tmpdir | \fB\-\-leave\-tmpdir]\fR
[\-\-move\-outputs | \fB\-\-leave\-outputs\fR | \fB\-\-copy\-outputs]\fR
[\-\-enable\-pull | \fB\-\-disable\-pull]\fR
[\-\-rdf\-serializer RDF_SERIALIZER]
[\-\-eval\-timeout EVAL_TIMEOUT]
[\-\-print\-rdf | \fB\-\-print\-dot\fR | \fB\-\-print\-pre\fR | \fB\-\-print\-deps\fR | \fB\-\-print\-input\-deps\fR | \fB\-\-pack\fR | \fB\-\-version\fR | \fB\-\-validate\fR | \fB\-\-print\-supported\-versions\fR | \fB\-\-print\-subgraph\fR | \fB\-\-print\-targets]\fR
[\-\-strict | \fB\-\-non\-strict]\fR [\-\-skip\-schemas]
[\-\-verbose | \fB\-\-quiet\fR | \fB\-\-debug]\fR [\-\-strict\-memory\-limit]
[\-\-timestamps] [\-\-js\-console]
[\-\-user\-space\-docker\-cmd CMD | \fB\-\-singularity\fR | \fB\-\-no\-container]\fR
[\-\-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 | \fB\-\-disable\-ga4gh\-tool\-registry]\fR
[\-\-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] ...
.PP
Reference executor for Common Workflow Language standards.
.SS "positional arguments:"
.TP
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 `workflow` argument is
optional.
.TP
inputs_object
path or URL to a YAML or JSON formatted description of
the required input values for the given
`cwl_document`.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.HP
\fB\-\-basedir\fR BASEDIR
.TP
\fB\-\-outdir\fR OUTDIR
Output directory, default current directory
.TP
\fB\-\-parallel\fR
[experimental] Run jobs in parallel.
.TP
\fB\-\-preserve\-environment\fR ENVVAR
Preserve specific environment variable when running
CommandLineTools. May be provided multiple times.
.TP
\fB\-\-preserve\-entire\-environment\fR
Preserve all environment variable when running
CommandLineTools.
.TP
\fB\-\-rm\-container\fR
Delete Docker container used by jobs after they exit
(default)
.TP
\fB\-\-leave\-container\fR
Do not delete Docker container used by jobs after they
exit
.TP
\fB\-\-tmpdir\-prefix\fR TMPDIR_PREFIX
Path prefix for temporary directories
.TP
\fB\-\-tmp\-outdir\-prefix\fR TMP_OUTDIR_PREFIX
Path prefix for intermediate output directories
.TP
\fB\-\-cachedir\fR CACHEDIR
Directory to cache intermediate workflow outputs to
avoid recomputing steps.
.TP
\fB\-\-rm\-tmpdir\fR
Delete intermediate temporary directories (default)
.TP
\fB\-\-leave\-tmpdir\fR
Do not delete intermediate temporary directories
.TP
\fB\-\-move\-outputs\fR
Move output files to the workflow output directory and
delete intermediate output directories (default).
.TP
\fB\-\-leave\-outputs\fR
Leave output files in intermediate output directories.
.TP
\fB\-\-copy\-outputs\fR
Copy output files to the workflow output directory,
don't delete intermediate output directories.
.TP
\fB\-\-enable\-pull\fR
Try to pull Docker images
.TP
\fB\-\-disable\-pull\fR
Do not try to pull Docker images
.TP
\fB\-\-rdf\-serializer\fR RDF_SERIALIZER
Output RDF serialization format used by \fB\-\-print\-rdf\fR
(one of turtle (default), n3, nt, xml)
.TP
\fB\-\-eval\-timeout\fR EVAL_TIMEOUT
Time to wait for a Javascript expression to evaluate
before giving an error, default 20s.
.TP
\fB\-\-print\-rdf\fR
Print corresponding RDF graph for workflow and exit
.TP
\fB\-\-print\-dot\fR
Print workflow visualization in graphviz format and
exit
.TP
\fB\-\-print\-pre\fR
Print CWL document after preprocessing.
.TP
\fB\-\-print\-deps\fR
Print CWL document dependencies.
.TP
\fB\-\-print\-input\-deps\fR
Print input object document dependencies.
.TP
\fB\-\-pack\fR
Combine components into single document and print.
.TP
\fB\-\-version\fR
Print version and exit
.TP
\fB\-\-validate\fR
Validate CWL document only.
.TP
\fB\-\-print\-supported\-versions\fR
Print supported CWL specs.
.TP
\fB\-\-print\-subgraph\fR
Print workflow subgraph that will execute (can combine
with \fB\-\-target\fR)
.TP
\fB\-\-print\-targets\fR
Print targets (output parameters)
.TP
\fB\-\-strict\fR
Strict validation (unrecognized or out of place fields
are error)
.TP
\fB\-\-non\-strict\fR
Lenient validation (ignore unrecognized fields)
.TP
\fB\-\-skip\-schemas\fR
Skip loading of schemas
.TP
\fB\-\-verbose\fR
Default logging
.TP
\fB\-\-quiet\fR
Only print warnings and errors.
.TP
\fB\-\-debug\fR
Print even more logging
.TP
\fB\-\-strict\-memory\-limit\fR
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 \fB\-\-memory\fR option.
.TP
\fB\-\-timestamps\fR
Add timestamps to the errors, warnings, and
notifications.
.TP
\fB\-\-js\-console\fR
Enable javascript console output
.TP
\fB\-\-user\-space\-docker\-cmd\fR 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'
.TP
\fB\-\-singularity\fR
[experimental] Use Singularity runtime for running
containers. Requires Singularity v2.3.2+ and Linux
with kernel version v3.18+ or with overlayfs support
backported.
.TP
\fB\-\-no\-container\fR
Do not execute jobs in a Docker container, even when
`DockerRequirement` is specified under `hints`.
.TP
\fB\-\-tool\-help\fR
Print command line help for tool
.TP
\fB\-\-relative\-deps\fR {primary,cwd}
When using \fB\-\-print\-deps\fR, print paths relative to
primary file or current working directory.
.TP
\fB\-\-enable\-dev\fR
Enable loading and running development versions of CWL
spec.
.TP
\fB\-\-enable\-ext\fR
Enable loading and running cwltool extensions to CWL
spec.
.TP
\fB\-\-default\-container\fR DEFAULT_CONTAINER
Specify a default docker container that will be used
if the workflow fails to specify one.
.TP
\fB\-\-no\-match\-user\fR
Disable passing the current uid to `docker run \fB\-\-user\fR`
.TP
\fB\-\-custom\-net\fR CUSTOM_NET
Passed to `docker run` as the '\-\-net' parameter when
NetworkAccess is true.
.TP
\fB\-\-enable\-ga4gh\-tool\-registry\fR
Enable resolution using GA4GH tool registry API
.TP
\fB\-\-disable\-ga4gh\-tool\-registry\fR
Disable resolution using GA4GH tool registry API
.TP
\fB\-\-add\-ga4gh\-tool\-registry\fR GA4GH_TOOL_REGISTRIES
Add a GA4GH tool registry endpoint to use for
resolution, default ['https://dockstore.org/api']
.TP
\fB\-\-on\-error\fR {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'.
.TP
\fB\-\-compute\-checksum\fR
Compute checksum of contents while collecting outputs
.TP
\fB\-\-no\-compute\-checksum\fR
Do not compute checksum of contents while collecting
outputs
.TP
\fB\-\-relax\-path\-checks\fR
Relax requirements on path names to permit spaces and
hash characters.
.TP
\fB\-\-make\-template\fR
Generate a template input object
.TP
\fB\-\-force\-docker\-pull\fR
Pull latest docker image even if it is locally present
.TP
\fB\-\-no\-read\-only\fR
Do not set root directory in the container as readonly
.TP
\fB\-\-overrides\fR OVERRIDES
Read process requirement overrides from file.
.TP
\fB\-\-target\fR TARGET, \fB\-t\fR TARGET
Only execute steps that contribute to listed targets
(can provide more than once).
.SS "Options for recording the Docker container identifier into a file.:"
.TP
\fB\-\-cidfile\-dir\fR CIDFILE_DIR
Store the Docker container ID into a file in the
specified directory.
.TP
\fB\-\-cidfile\-prefix\fR CIDFILE_PREFIX
Specify a prefix to the container ID filename. Final
file name will be followed by a timestamp. The default
is no prefix.
.SH "SEE ALSO"
.br
http://commonwl.org
.br
http://wiki.debian.org/CommonWorkflowLanguage