Fix crash related to skipped subworkflows

[simleo]

Some steps can be skipped due to the presence of a when condition. This can lead to an entire subworkflow not being executed, which was not handled by patch_workflow_input_collection (the subworkflow is listed in the prospective provenance but there's no corresponding action in the retrospective provenance). This PR fixes that.

With this fix, the RO bundle provided in #33 can be converted successfully.

Note that in the output RO-Crate the subworkflow and the corresponding step are listed in the RO-Crate, while no corresponding action is listed (similarly to CWLProv).

[codecov]

Codecov Report

Patch coverage: 100.00% and project coverage change: +0.07 🎉

Comparison is base (ecd0a71) 97.26% compared to head (78bdaaf) 97.34%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #45      +/-   ##
==========================================
+ Coverage   97.26%   97.34%   +0.07%     
==========================================
  Files          11       11              
  Lines        1790     1805      +15     
==========================================
+ Hits         1741     1757      +16     
+ Misses         49       48       -1     

Impacted Files	Coverage Δ
src/runcrate/convert.py	97.75% <100.00%> (+0.18%)	⬆️
tests/test_cwlprov_crate_builder.py	99.88% <100.00%> (+<0.01%)	⬆️

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