Provided by: cwltool_1.0.20180302231433-1_all bug


       cwltool - Refefence executor for Common Workflow Language


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

              [--preserve-environment  ENVVAR  | --preserve-entire-environment] [--rm-container |
              --leave-container]     [--record-container-id]     [--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]   [--strict   |
              --non-strict]  [--skip-schemas]  [--verbose  |  --quiet  |  --debug] [--timestamps]
              [--js-console]  [--user-space-docker-cmd  CMD  |  --singularity  |  --no-container]
              [--tool-help]   [--relative-deps   {primary,cwd}]   [--enable-dev]   [--enable-ext]
              [--default-container    DEFAULT_CONTAINER]    [--no-match-user]     [--disable-net]
              [--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] [cwl_document] ...

       Reference executor for Common Workflow Language standards.

   positional arguments:
              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.

              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

              [experimental]  Run  jobs  in  parallel.  Does  not   currently   keep   track   of
              ResourceRequirements like the number of coresor memory and can overload this system

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

              Preserve all environment variable when running CommandLineTools.

              Delete Docker container used by jobs after they exit (default)

              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.

              Delete intermediate temporary directories (default)

              Do not delete intermediate temporary directories

              Move output files to the workflow output directory and delete  intermediate  output
              directories (default).

              Leave output files in intermediate output directories.

              Copy  output  files  to  the  workflow  output directory, don't delete intermediate
              output directories.

              Try to pull Docker images

              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 corresponding RDF graph for workflow and exit

              Print workflow visualization in graphviz format and exit

              Print CWL document after preprocessing.

              Print CWL document dependencies.

              Print input object document dependencies.

       --pack Combine components into single document and print.

              Print version and exit

              Validate CWL document only.

              Print supported CWL specs.

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

              Lenient validation (ignore unrecognized fields)

              Skip loading of schemas

              Default logging

              Only print warnings and errors.

              Print even more logging

              Add timestamps to the errors, warnings, and notifications.

              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'

              [experimental] Use Singularity runtime for running containers. Requires Singularity
              v2.3.2+ and Linux with kernel version v3.18+ or with overlayfs support backported.

              Do not execute jobs  in  a  Docker  container,  even  when  `DockerRequirement`  is
              specified under `hints`.

              Print command line help for tool

       --relative-deps {primary,cwd}
              When  using  --print-deps,  print paths relative to primary file or current working

              Enable loading and running development versions of CWL spec.

              Enable loading and running cwltool extensions to CWL spec.

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

              Disable passing the current uid to `docker run --user`

              Use   docker's  default  networking  for  containers;  the  default  is  to  enable

       --custom-net CUSTOM_NET
              Will be passed to `docker run` as the '--net' parameter. Implies '--enable-net'.

              Enable resolution using GA4GH tool registry API

              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

       --on-error {stop,continue}
              Desired  workflow  behavior when a step fails. One of 'stop' or 'continue'. Default
              is 'stop'.

              Compute checksum of contents while collecting outputs

              Do not compute checksum of contents while collecting outputs

              Relax requirements on path names to permit spaces and hash characters.

              Generate a template input object

              Pull latest docker image even if it is locally present

              Do not set root directory in the container as readonly

       --overrides OVERRIDES
              Read process requirement overrides from file.

   Options for recording the Docker container identifier into a file:
              If enabled, store the Docker container  ID  into  a  file.   See  --cidfile-dir  to
              specify the directory.

       --cidfile-dir CIDFILE_DIR
              Directory  for  storing  the  Docker container ID file.  The default is the current

       --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.