Mismatched paths when specifying data directory and output test folder

[stxue1]

I'm having trouble running the run_tests_miniwdl.py script after extracting the test files out of the spec with extract_tests.py.

I'm running this command to extract the tests:

python extract_tests.py -i path/to/SPEC.md -d path/to/data/ -O tests

But when I run the run_tests_miniwdl.py script with:

python run_tests_miniwdl.py -T tests

I get a CalledProcessError. It looks like this line changes the running directory for miniwdl, but the WDL paths specified in test_config.json do not reflect this change. For example:

...
    "id": "hello",
    "path": "tests/hello.wdl",
...

Thus, the value passed into the cwd is tests/data, which eventually leads to the script being unable to find the file:

[Errno 2] No such file or directory: 'tests/hello.wdl'

I think this issue will occur whenever a data directory is specified and when an output directory is given.