Provided by: cwltool_3.1.20220224085855-1_all bug


       cwltool - Refefence executor for Common Workflow Language


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

              [--log-dir     LOG_DIR]     [--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  |  --make-template]  [--strict  |  --non-strict]  [--skip-schemas]
              [--no-doc-cache    |    --doc-cache]    [--verbose    |    --quiet    |    --debug]
              [--strict-memory-limit]    [--strict-cpu-limit]    [--timestamps]    [--js-console]
              [--disable-js-validation]       [--js-hint-options-file       JS_HINT_OPTIONS_FILE]
              [--user-space-docker-cmd   CMD   |   --udocker   |   --singularity   |  --podman  |
              --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]
              [--force-docker-pull] [--no-read-only] [--overrides OVERRIDES] [--target  TARGET  |
              --single-step  SINGLE_STEP  |  --single-process  SINGLE_PROCESS] [--mpi-config-file
              MPI_CONFIG_FILE] [cwl_document] ...

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

   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 `cwl_document` argument is optional.

              path or URL to a YAML or JSON formatted description of the  required  input  values
              for the given `cwl_document`.

       -h, --help
              show this help message and exit

       --basedir BASEDIR

       --outdir OUTDIR
              Output directory. The default is the current directory.

       --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

              [experimental] Run jobs in parallel.

       --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

              Preserve all environment variables when running CommandLineTools without a software

              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. If --tmpdirprefix 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-outdir-prefix TMP_OUTDIR_PREFIX
              Path  prefix  for  intermediate  output  directories.   Defaults  to  the  value of

       --cachedir CACHEDIR
              Directory to cache intermediate workflow outputs to avoid recomputing steps. Can be
              very helpful in the development and troubleshooting of CWL documents.

              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 and  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.

              Print   workflow  subgraph  that  will  execute.  Can  combined  with  --target  or

              Print targets (output parameters)

              Generate a template input object

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

              Lenient validation (ignore unrecognized fields)

              Skip loading of schemas

              Disable disk cache for documents loaded over HTTP

              Enable disk cache for documents loaded over HTTP

              Default logging

              Only print warnings and errors.

              Print even more logging

              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.

              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.

              Add timestamps to the errors, warnings, and notifications.

              Enable javascript console output

              Disable javascript validation.

       --js-hint-options-file JS_HINT_OPTIONS_FILE
              File  of  options  to  pass   to   jshint.   This   includes   the   added   option

       --user-space-docker-cmd CMD
              (Linux/OS X only) Specify the path to udocker. Implies --udocker

              (Linux/OS  X  only)  Use  the udocker runtime for running containers (equivalent to

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

              [experimental] Use Podman runtime for running containers.

              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 unofficial development versions of the CWL standards.

              Enable loading and running 'cwltool:' extensions to the CWL standards.

              Enable logging color (default enabled)

              Disable colored logging (default false)

       --default-container DEFAULT_CONTAINER
              Specify  a  default  software  container  to  use for any CommandLineTool without a

              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.

              Enable tool resolution using GA4GH tool registry API

              Disable tool 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' (do not submit any  more
              steps)  or  'continue'  (may  submit  other  steps that are not downstream from the
              error). 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.

              Pull latest software container 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.

       --target TARGET, -t TARGET
              Only execute steps that contribute to listed targets (can  be  provided  more  than

       --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.

       --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.

   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.