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