Fix crash related to skipped subworkflows #45
Merged
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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 bypatch_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).