miniwdl run command line

For details & configuration see:

usage: miniwdl run [-h] [-i INPUT.json] [--empty input_key] [--none input_key]
                   [--task TASK_NAME] [-j] [-d DIR] [--error-json]
                   [-o OUT.json] [-v] [--no-color] [--log-json] [--cfg FILE]
                   [--runtime-defaults JSON] [--no-cache]
                   [--env VARNAME[=VALUE]] [--copy-input-files]
                   [--copy-input-files-for TASK_NAME] [--as-me] [-p DIR]
                   [--no-outside-imports] [--no-quant-check] [--debug]
                   URI [input_key=value [input_key=value ...]]

Positional Arguments

URI WDL document filename/URI
 Workflow inputs. Optional space between = and value. For arrays repeat, key=value1 key=value2 …


-i, --input Cromwell-style input JSON object, filename, or -; command-line inputs will be merged in
--empty explicitly set a string input to the empty string OR an array input to the empty array
--none explicitly set an optional input to None (to override a default)
--task name of task to run (for WDL documents with multiple tasks & no workflow)
-j, --json just print Cromwell-style input JSON to standard output, then exit


-d, --dir directory under which to create a timestamp-named subdirectory for this run (defaults to current working directory); supply ‘.’ or ‘some/dir/.’ to instead run in this directory exactly
--error-json upon failure, print error information JSON to standard output (in addition to standard error logging)
-o write JSON output/error to specified file instead of standard output (implies –error-json)


-v, --verbose increase logging detail & stream tasks’ stderr
--no-color disable colored logging and status bar on terminal (also set by NO_COLOR environment variable)
--log-json write all logs in JSON


--cfg configuration file to load (in preference to file named by MINIWDL_CFG environment, or XDG_CONFIG_{HOME,DIRS}/miniwdl.cfg)
 default runtime settings for all tasks (JSON filename or literal object e.g. ‘{“maxRetries”:2}’)
--no-cache override any configuration enabling cache lookup for call outputs & downloaded files
--env Environment variable to pass through to [or set outright in] all task environments (can supply multiple times; warning, non-portable side channel)
 copy input files for each task and mount them read/write (unblocks task commands that mv/rm/write them)
 copy input files only for specifically named task (can supply multiple times)
--as-me run all containers as the invoking user uid:gid (more secure, but potentially blocks task commands e.g. apt-get)


-p, --path local directory to search for imports (can supply multiple times)
 deny local imports from outside directory of main WDL file (or –path)
 relax static typechecking of optional types, and permit coercion of T to Array[T] (discouraged; for backwards compatibility with older WDL)


--debug maximally verbose logging & exception tracebacks