$ java -jar dxCompiler.jar version
$ java -jar dxCompiler.jar help
java -jar dxCompiler.jar <action> <parameters> [options]
Prints the dxCompiler version.
Prints the current dxCompiler configuration.
Generate the JSON execution tree for a given DNAnexus workflow ID.
The workflow needs to be have been previously compiled by dxCompiler.
-pretty Print exec tree in "pretty" text format instead of JSON.
compile <WDL or CWL file>
Compile a WDL or CWL file to a DNAnexus workflow or applet.
-archive Archive older versions of applets.
Compilation mode - If not specified, the compilation
mode is "All" and the compiler will translate WDL or CWL
inputs into DNAnexus workflows and tasks.
Use "IR" if you only want to parse CWL or WDL files and
convert standard-formatted input files to DNAnexus JSON
input format without performing full compilation.
-defaults <string> JSON file with standard-formatted default values.
The default instance type to use for "helper" applets
that perform runtime evaluation of instance type
requirements. This instance type is also used when
the '-instanceTypeSelection dynamic' option is set.
This value is overriden by any defaults set in set in the
JSON file specified by '-extras'.
-destination <string> Full platform path (project:/folder).
Print a JSON representation of the workflow.
-extras <string> JSON file with extra options (see documentation).
-inputs <string> JSON file with standard-formatted input values. May be
specified multiple times. A DNAnexus JSON input file is
generated for each standard input file.
Whether to select instance types at compile time for tasks with
runtime requirements that can all be statically evaluated
(the default "static" option), or to defer instance type
selection in such cases to runtime (the "dynamic" option).
Using static instance type selection can save time, but it
requires the same set of instances to be accessible during WDL/CWL
compilation and during the runtime of the generated applets and
workflows. Use the "dynamic" option if you plan on creating global
DNAnexus workflows or cloning the generated workflows between
DNAnexus organizations with different available instance types.
-locked Create a locked workflow. When running a locked workflow,
input values may only be specified for the top-level workflow.
-leaveWorkflowsOpen Leave created workflows open (otherwise they are closed).
-p | -imports <string> Directory to search for imported WDL or CWL files. May be specified
-projectWideReuse Look for existing applets/workflows in the entire project
before generating new ones. The default search scope is the
-reorg Reorganize workflow output files.
How much debug information to write to the job log at runtime.
Log the minimum (0), intermediate (1, the default), or all
debug information (2, for internal debugging).
-separateOutputs Store the output files of each call in a separate folder. The
default behavior is to put all outputs in the same folder.
Whether to mount all files with dxfuse (do not use the
download agent), to mount no files with dxfuse (only use
download agent), or to respect the per-file settings in WDL
parameter_meta sections (default).
-useManifests Use manifest files for all workflow and applet inputs and
outputs. Implies -locked.
-waitOnUpload Whether to wait for each file upload to complete.
DNAnexus Native call Interface. Creates stubs for calling DNAnexus executables
(apps/applets/workflows), and stores them as WDL tasks in a local file. Enables
calling existing platform executables without modification.
Option 'include' includes both apps and applets, 'exclude'
excludes apps and generates applet stubs only, 'only'
generates app stubs only.
-f | force Delete any existing output file.
-o <path> Destination file for WDL task definitions (defaults to
-path <string> Name of a specific app or a path to a specific applet.
-r | recursive Search recursively for applets in the target folder.
-folder <string> Platform folder (defaults to '/').
-project <string> Platform project (defaults to currently selected project).
-language <string> [ver] Which language to use? May be WDL or CWL. You can optionally
specify a version. Currently: i. WDL: draft-2, 1.0, and 1.1, and
ii. CWL: 1.2 are supported and WDL development is partially
supported. The default is to auto-detect the language from the
-quiet Do not print warnings or informational outputs.
-verbose Print detailed logging.
-verboseKey <module> Print verbose output only for a specific module. May be
specified multiple times.
-logFile <path> File to use for logging output; defaults to stderr.