Provided by: cwltool_1.0.20180302231433-1_all bug

NAME

       cwltool - Refefence executor for Common Workflow Language

DESCRIPTION

       usage: __main__.py [-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:
       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.  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-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.

       --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

       --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
              v2.3.2+ 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.

       --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`

       --disable-net
              Use   docker's  default  networking  for  containers;  the  default  is  to  enable
              networking.

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

       --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:8443']

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

   Options for recording the Docker container identifier into a file:
       --record-container-id
              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
              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