Docker and CWL databases type "string"

[mberacochea]

Running the pipeline using docker is currently blocked by the databases paths being strings instead of Directory|File.

The paths change to string was required due to some issues with Toil and the EBI cluster.

We are currently working to fix this problem and make the pipeline fully compatible with docker. The current hacky workaround to this problem is to patch the docker.py file in CWL and add the databases' folder path hardcoded.

The patch only works for Toil[CWL] and cwltool.

Patch for docker.py.

self.append_volume(runtime, "<PATH to DBS>", "/data/databases", writable=False)

[KateSakharova]

@mberacochea Martin, it is possible to use several types for inputs For example,

type: [ string, File ]

I think it will solve our problem without any significant changes :)

[mberacochea]

Brilliant @KeteSakharova , I'll give that a try.

[KateSakharova]

I'm trying to fix that in docker-databases-paths-fix branch but I bumped into similar issue like in https://github.com/common-workflow-language/cwltool/issues/1285