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] [-v]
                   [--no-color] [--log-json] [--cfg FILE]
                   [--runtime-defaults JSON] [--no-cache] [--copy-input-files]
                   [--as-me] [--no-quant-check] [-p DIR] [--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)

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
--copy-input-files
 copy input files for each task and mount them read/write (unblocks task commands that mv/rm/write them)
--as-me run all containers as the invoking user uid:gid (more secure, but potentially blocks task commands e.g. apt-get)

language

--no-quant-check
 relax static typechecking of optional types, and permit coercion of T to Array[T] (discouraged; for backwards compatibility with older WDL)
-p, --path local directory to search for imports

debugging

--debug maximally verbose logging & exception tracebacks