allow vsearch merge-pairs to output unmerged reads

[colinvwood]

No description provided.

[gregcaporaso]

I'm realizing now that this is going to change the interface of merge-pairs.

I see two ways to go here:

1. Merge this just after the 2023.11 release, and include in the 2023.11 release notes that this interface will be changing in the first release of 2024.
2. We could add a parameter to q2_vsearch._merge_pairs.merge_pairs that toggles whether we create the unmerged reads output, and then have two actions that call that function - one that doesn't output the unmerged reads (i.e., the existing action) and a second action that does output the unmerged reads.

I'm leaning toward Option 1, to avoid action-bloat. Thoughts on this @colinvwood, @ebolyen?

[colinvwood]

do we always warn of these sorts of changes one release cycle beforehand?

[gregcaporaso]

Generally, yes - we like to announce interface changes one cycle before making them (and this changes the interface by adding a new required output - so analysis workflows that call this action will fail until the new output is integrated in the workflow). That gives folks time to update any automated workflows.

[colinvwood]

I agree that the first option seems like the better way to go

[colinvwood]

I wonder though, since vsearch has never been part of the shotgun distribution, wouldn't adding it with these changes to that distribution not constitute a change of interface (but an introduction of one which is happening either way)? and the amplicon distribution can wait a cycle?

but that might not be possible because we would need two branches on vsearch one for each distribution release

I guess we could release amplicon then merge this then release shotgun

[gregcaporaso]

Good point that it would be an interface change for the amplicon distro but not the shotgun distro. I'd be good with that plan, but I just wonder if it creates a lot of headaches for the release. Let's discuss in the engineering meeting today.

[colinvwood]

We're planning on merging just after the 2023.12 release for both distributions.

[gregcaporaso]

Looks great overall. Just a couple of questions regarding test data, and one request for a test.

[gregcaporaso]

Thanks @colinvwood!