miniwdl run command line

For details & configuration see: https://miniwdl.readthedocs.io/en/latest/runner_reference.html

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
input_key=value
	Workflow inputs. Optional space between = and value. For arrays repeat, key=value1 key=value2 …

input

-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

output

-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)

logging

-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

configuration

--cfg	configuration file to load (in preference to file named by MINIWDL_CFG environment, or XDG_CONFIG_{HOME,DIRS}/miniwdl.cfg)
--runtime-defaults
	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
	copy input files for each task and mount them read/write (unblocks task commands that mv/rm/write them)
--copy-input-files-for
	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)

language

-p, --path	local directory to search for imports (can supply multiple times)
--no-outside-imports
	deny local imports from outside directory of main WDL file (or –path)
--no-quant-check
	relax static typechecking of optional types, and permit coercion of T to Array[T] (discouraged; for backwards compatibility with older WDL)

debugging

--debug

maximally verbose logging & exception tracebacks