Fix for rerunning tool with workflow resume that is part of a collection.

[blankenberg]

The special casing of |__identifier__ that occurs here and elsewhere in the code is less than ideal.

[nsoranzo]

This should be a partial fix for #2235, according to @blankenberg's comments from IRC:

yes, this should fix the things inside the collection and downstream
hmm, actually, looks like it doesn't fix it in the original collection, but the downstream collections update
so if the one failure occurs a tool or more upstream, the final collections will be ok
if the failure occurs on the final collection, #3019 doesn't help

[blankenberg]

Any other comments on this PR?

[martenson]

afaik This should allow resuming a workflow that has been waiting on a failed dataset in a collection. It will rerun the failed dataset (but not update it in the collection) and allow the downstream tools to be run/unpaused.
Thank you @blankenberg !