Allow pending inputs in some collection operation tools

[mvdbeek]

For those tools where it makes sense. We can't of course do this for tools that filter outputs based on dataset size or dataset state, or tools that make decisions based on extra datasets (e.g text files with new identifiers or tags).

As mentioned inline, we could allow more tools to run with pending input collections, but that doesn't work if we need to read an additional file from disk. To be more flexible for those cases we could add more special casing or we could let the job handler loop handle the waiting for datasets for us, neither of which seems worth doing right now.

Does a bit of what is requested in #15879

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[assuntad23]

👍🏻

[davelopez]

Thank you!