macOS: task input files sporadically fail to mount (zero length)

The attached workflow returns the correct output sometimes and other times does not. In the failure case it is because the input file is not correctly staged in the task’s work/ directory - the staged file is empty rather than containing the correct content. When I set --copy-input-files it always works correctly.

The exact command line I use is:

miniwdl run --error-json --copy-input-files -i input.json -p submodule test.wdl

and input.json is:

{"cat_file.in_txt": "data/in.txt", "cat_file.in_int": 1}

failing_test.zip

[nh13]

Chiming in that I hit this too, and using the “legacy osxfs files sharing” fixed it for me too.

[mlin]

I can confirm that disabling this setting, Docker for Mac > Preferences > Experimental Features > Use gRPC for file sharing makes the miniwdl unit test suite work well on my MacBook, while it’s busted with that setting on as default.

(image credit @tomkinsc; cc @lynnlangit)

One can google a variety of issues people have opened with either alternative of that setting, so I suppose we just have to make do with this pitfall for the time being =/