It looks like part of the problem here is that you are trying to use an input bai that doesn't exist in your above degradation.cwl script. You could probably do one of two things:

1) Modify degradation.cwl to take the .bai file explicitly as input then use your workflow.cwl as is just by adding an input as bai: File to inputs of degradation.cwl. This may require use of InitialWorkDirRequirement, but I'm not sure so I'd test this out first before adding it.

degradation.cwl

inputs:
  bai: File
  annotation:
    type: File
    inputBinding:
     position: 2
     prefix: -a
  bam:
    type: File
    inputBinding:
     position: 1
     prefix: -n
    secondaryFiles: .bai

OR

2) Modify your workflow.cwl to return an object that has the secondary file as a secondary file. You can either add a step between bam_indexing and degradation that is an Expression tool that returns a File object + secondary file. A potentially easier method, depending on how index_bam.cwl is written, you can probably use .bam file as input and return as output the bam file + bai as its secondary file instead of returning the bai alone. Like so

index_bam. cwl

outputs:
  indexed_bam:
    type: File
    secondaryFiles: .bai
    outputBinding:
      glob: $(inputs.bam.basename)

If index_bam.cwl doesn't work like this, then I would add the expression tool, but try one of these suggestions for now and see how it works. My preference is for option (2), but let me know what ends up working if anything. And if it doesn't or doesn't make sense, you'll need to post your full CWL document to help me understand better why it doesn't work.