Mike Lin

The spec shows this stuff being used in `command` and `output` declarations, and isn't crystal clear whether it's accessible in `input`, non-input, and `requirements` declarations. We probably shouldn't due to...

Agree this is an issue since [the spec says](https://github.com/openwdl/wdl/blob/wdl-1.1/SPEC.md#stripping-leading-whitespace) > When a command template is evaluated, the execution engine *first* strips out all common leading whitespace. (emphasis mine) It would...

Note to self: we implemented the necessary logic for multistrings, https://github.com/chanzuckerberg/miniwdl/blob/4a6157fb43b68691ca2661c6c7264b050cc77131/WDL/_parser.py#L154 Need to "backport" that to task commands. Perhaps it similarly makes sense to do this during parsing rather than...

Spec clarification probably needed here: > When a value is declared with the `env` modifier, it becomes the execution engine's responsibility to escape the string thus preventing any sort of...

Don't forget runtime override of hints -- see https://github.com/chanzuckerberg/miniwdl/issues/757#issuecomment-3488368016 for details of the similar runtime/requirements override feature (but here we have workflow hints too)

@markjschreiber Great stuff, thank you! #667 It looks like there are some remaining issues in the integration tests we have for `miniwdl check` (run with `prove -v tests/check.t`)

@stxue1 thanks for reporting, I have not tried Docker Desktop on Linux before so I'll need to look into this further. I'm surprised that it leaves files created by the...

@stxue1 Belated follow-up as I was looking into this a little. It might help to set the miniwdl configuration option [`[file_io] chown = false`](https://github.com/chanzuckerberg/miniwdl/blob/1bc3776e65d3069c2e890fa73aee0c5e44861e69/WDL/runtime/config_templates/default.cfg#L85-L89) (equivalently environment variable `MINIWDL__FILE_IO__CHOWN=false`. I think...