cwltool validate will pass workflows with fatal issues in included processes

[ghost]

cwltool 3.0.20200324120055

Consider the following workflow: https://github.com/NCI-GDC/gdc-dnaseq-cwl/blob/18affdd927cc388fab2c113dc2ec6df782af2a52/workflows/bamfastq_align/transform.cwl

This passes cwltool --validate. However, there is an issue with an enclosed workflow: The workflow gdc-dnaseq-cwl/workflows/bamfastq_align/fastq_clean_pe.cwl does not supply a required input reads_in_memory to the tool gdc-dnaseq-cwl/tools/fastq_cleaner_pe.cwl

[ghost]

@tetron , @mr-c I feel this is an important issue to fix because we've run into several workflows in the wild that fail to run because they pass validation on the top level but contain errors in child processes.

[mr-c]

INFO /home/michael/cwltool/env3.8/bin/cwltool 3.0.20201205091845
ERROR Tool definition failed validation:
https://github.com/NCI-GDC/gdc-dnaseq-cwl/blob/18affdd927cc388fab2c113dc2ec6df782af2a52/workflows/bamfastq_align/transform.cwl:91:65: mapping values are
                                                                                                                                      not allowed here

[mr-c]

https://github.com/NCI-GDC/gdc-dnaseq-cwl/blob/18affdd927cc388fab2c113dc2ec6df782af2a52/workflows/bamfastq_align/transform.cwl#L91 doesn't look invalid to my eyes