I wasn't sure if this was a question or a bug, so decided to first post a question about it. I can file an issue if it's confirmed to be a bug.
It looks like files are not mounted properly in directories when they're passed from one tool to another. Note that the files are tracked properly by CWL; they're just not mapped to the directory.
An example workflow is shown below. The output of
ls is just an empty directory. The expected output is a full list of files and their subdirectories. I ran it using
cwl-runner v1.0 and
cwltool v1.0.20190831161204. Is there something that I'm missing when operating on directories in CWL?
The workaround is to explicitly loop through the
listing inside the input directory and map them using