Provided by: cwltool_1.0.20190815141648+dfsg-1ubuntu2_all bug

NAME

       cwltool - Refefence executor for Common Workflow Language

DESCRIPTION

       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]      [--enable-color      |      --disable-color]
              [--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:
       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.

       inputs_object
              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

       --parallel
              [experimental] Run jobs in parallel.

       --preserve-environment ENVVAR
              Preserve  specific  environment  variable  when  running  CommandLineTools.  May be
              provided multiple times.

       --preserve-entire-environment
              Preserve all environment variable when running CommandLineTools.

       --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

       --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.

       --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, don't delete intermediate
              output directories.

       --enable-pull
              Try to pull Docker images

       --disable-pull
              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-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 combine with --target)

       --print-targets
              Print targets (output parameters)

       --strict
              Strict validation (unrecognized or out of place fields are error)

       --non-strict
              Lenient validation (ignore unrecognized fields)

       --skip-schemas
              Skip loading of schemas

       --verbose
              Default logging

       --quiet
              Only print warnings and errors.

       --debug
              Print even more logging

       --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.

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

       --js-console
              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'

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

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

       --tool-help
              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-dev
              Enable loading and running development versions of CWL spec.

       --enable-ext
              Enable loading and running cwltool extensions to CWL spec.

       --enable-color
              Enable colored logging (default true)

       --disable-color
              Disable colored logging (default false)

       --default-container DEFAULT_CONTAINER
              Specify a default docker container that will be  used  if  the  workflow  fails  to
              specify one.

       --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.

       --enable-ga4gh-tool-registry
              Enable resolution using GA4GH tool registry API

       --disable-ga4gh-tool-registry
              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
              ['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.

       --make-template
              Generate a template input object

       --force-docker-pull
              Pull latest docker image even if it is locally present

       --no-read-only
              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.

SEE ALSO

       http://commonwl.org
       http://wiki.debian.org/CommonWorkflowLanguage