Upgrade a cwl 1.2 workflow fails

[golharam]

Using cwl-upgrader-1.2.2

$ cwl-upgrader rsem-merge.cwl
Processing rsem-merge.cwl
Unsupported cwlVersion: v1.2
Traceback (most recent call last):
File "/Users/golharr/workspace/NGS/RNASeq/env/bin/cwl-upgrader", line 8, in
sys.exit(main())
File "/Users/golharr/workspace/NGS/RNASeq/env/lib/python3.6/site-packages/cwlupgrader/main.py", line 59, in main
return run(parse_args(args))
File "/Users/golharr/workspace/NGS/RNASeq/env/lib/python3.6/site-packages/cwlupgrader/main.py", line 80, in run
document, args.v1_only, args.v1_1_only, args.dir, imports
File "/Users/golharr/workspace/NGS/RNASeq/env/lib/python3.6/site-packages/cwlupgrader/main.py", line 118, in upgrade_document
process_imports(document, imports, inner_updater, output_dir)
UnboundLocalError: local variable 'inner_updater' referenced before assignment

I would expect this to validate the cwl 1.2 workflow and ensure nothing is wrong, since there isn't an upgrade needed.

[tetron]

Hi @golharam

Yes that's an unfortunate oversight, running the upgrader on a v1.2 document should be a no-op but instead it fails because it didn't choose an updater (because there's nothing to update). I'll see about whipping up a quick fix.

[mr-c]

Fixed in #94