Allowing directories to be assigned as a File type

[kmhernan]

Hello,

It appears that cwltool no longer allows you to assign a path as a File, which then makes it difficult to mount a directory to the docker run. This is especially problematic for things like variant annotation software which often have a particular directory structure containing 100's of annotation files.

It seems like the commit present here is potentially the culprit. This functionality worked with cwl version 1.0.20160129183049 but it definitely doesn't work in the current one. How can we handle this issue?

[mr-c]

Hello @kmhernan and thank you for your report.

This behaviour change of cwltool is to match the standard. Over in common-workflow-language/common-workflow-language#172 is a great proposal from @tetron to add functionality to do what you're asking for. We would then implement it in cwltool.

I'm going to close this issue; please let us know in common-workflow-language/common-workflow-language#172 if it works for you.