cwltool --print-deps fails with workflows having namespaced location steps

[José María Fernández]

I have been testing to "print" the list of dependencies of several workflows which have some of its steps declarations outside their workflow repository. I need them to be able to capture the list of all the CWL URLs involved in a workflow.

For instance, if you test next workflow:

git clone https://github.com/Sage-Bionetworks-Challenges/data-to-model-challenge-workflow
cd data-to-model-challenge-workflow
cwltool --print-deps --relative-deps primary workflow.cwl

it provides the list of both local and remote cwl files.

But, with workflows where the base location is declared as a namespace, and then the namespace is used to declare the step location in a shorter way, next operation is failing:

git clone https://github.com/pvanheus/lukasa/
cd lukasa
cwltool --print-deps --relative-deps primary protein_evidence_mapping.cwl

ERROR Tool definition failed validation:
Unsupported scheme in url: bio-cwl-tools:samtools/samtools_faidx.cwl

All the tests have been with cwltool 3.1.20221109155812 .

[José María Fernández]

Uppps!!! I have just realized I opened the issue in the wrong repository (too many open tabs).

Sorry!!!!