-h2. Command line options
-
-table(table table-bordered table-condensed).
-|_. Option |_. Description |
-| --basedir BASEDIR| Base directory used to resolve relative references in the input, default to directory of input object file or current directory (if inputs piped/provided on command line).|
-| --version| Print version and exit|
-| --verbose| Default logging|
-| --quiet| Only print warnings and errors.|
-| --debug| Print even more logging|
-| --tool-help| Print command line help for tool|
-| --enable-reuse|Enable job reuse (default)|
-| --disable-reuse|Disable job reuse (always run new jobs).|
-| --project-uuid UUID| Project that will own the workflow jobs, if not provided, will go to home project.|
-| --output-name OUTPUT_NAME|Name to use for collection that stores the final output.|
-| --output-tags OUTPUT_TAGS|Tags for the final output collection separated by commas, e.g., '--output-tags tag0,tag1,tag2'.|
-| --ignore-docker-for-reuse|Ignore Docker image version when deciding whether to reuse past jobs.|
-| --submit| Submit workflow to run on Arvados.|
-| --local| Control workflow from local host (submits jobs to Arvados).|
-| --create-template| (Deprecated) synonym for --create-workflow.|
-| --create-workflow| Create an Arvados workflow (if using the 'containers' API) or pipeline template (if using the 'jobs' API). See --api.|
-| --update-workflow UUID|Update an existing Arvados workflow or pipeline template with the given UUID.|
-| --wait| After submitting workflow runner job, wait for completion.|
-| --no-wait| Submit workflow runner job and exit.|
-| --api WORK_API| Select work submission API, one of 'jobs' or 'containers'. Default is 'jobs' if that API is available, otherwise 'containers'.|
-| --compute-checksum| Compute checksum of contents while collecting outputs|
-| --submit-runner-ram SUBMIT_RUNNER_RAM|RAM (in MiB) required for the workflow runner job (default 1024)|
-| --name NAME| Name to use for workflow execution instance.|
-
-h3. Specify workflow and output names
-
-Use the @--name@ and @--output-name@ options to specify the name of the workflow and name of the output collection.
+h3(#docker). Docker images
+
+Docker images referenced by the workflow must be uploaded to Arvados. This requires @docker@ to be installed and usable by the user running @arvados-cwl-runner@. If the image is not present in the local Docker instance, @arvados-cwl-runner@ will first attempt to pull the image using @docker pull@, then upload it.
+
+If there is already a Docker image in Arvados with the same name, it will use the existing image. In this case, the submitter will not use Docker.
+
+The @--match-submitter-images@ option will check the id of the image in the local Docker instance and compare it to the id of the image already in Arvados with the same name and tag. If they are different, it will choose the image matching the local image id, which will be uploaded it if necessary. This helpful for development, if you locally rebuild the image with the 'latest' tag, the @--match-submitter-images@ will ensure that the newer version is used.
+
+h3(#dependencies). Dependencies
+
+Dependencies include collections and Docker images referenced by the workflow. Dependencies are automatically uploaded by @arvados-cwl-runner@ if they are not present or need to be updated. When running a workflow, dependencies that already exist somewhere on the Arvados instance (from a previous upload) will not be uploaded or copied, regardless of the project they are located in. Sometimes this creates problems when sharing a workflow run with others. In this case, use @--copy-deps@ to indicate that you want all dependencies to be copied into the destination project (specified by @--project-uuid@).
+
+h3. Command line options
+
+See "arvados-cwl-runner options":{{site.baseurl}}/user/cwl/cwl-run-options.html
+
+h2(#registering). Registering a workflow to use in Workbench
+
+Use @--create-workflow@ to register a CWL workflow with Arvados. Use @--project-uuid@ to upload the workflow to a specific project, along with its dependencies. You can share the workflow with other Arvados users by sharing that project. You can run the workflow by clicking the <span class="btn btn-sm btn-primary">+ NEW</span> → <i class="fa fa-fw fa-gear"></i> *Run a process* menu items on the Workbench, and on the command line by UUID.