Update to topic isoseq3/tag

[bhargava-morampalli]

PR checklist

Closes #11823

The deprecated isoseq3 meta-package makes its isoseq dependency to 4.3.0
while the container stays at 4.0.0, breaking the
conda snapshot tests. Switch to the isoseq package/container at 4.0.0, matching the isoseq/cluster and isoseq/refine modules.

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[SPPearce]

Hmm, should this module just be isoseq/tag, not isoseq3/tag?

[bhargava-morampalli]

Hmm, should this module just be isoseq/tag, not isoseq3/tag?

Yes, isoseq3 is now a deprecated meta-package that simply wraps isoseq. When I tested locally, installing isoseq3 just creates a symlink to isoseq. Another problem is that the isoseq3 meta-package forces isoseq to 4.3.0 regardless of the version you request, while the container image sits at 4.0.0 and this mismatch is what broke the conda snapshot tests. I used isoseq version 4.0.0 (matching isoseq/cluster and isoseq/refine) and it fixed the issue confirming the problem.
For changing isoseq3/tag into the existing isoseq submodule structure alongside cluster and refine, that seemed like the logical thing to do, but I haven't worked with these tools before so I wasn't confident enough to just go ahead with it. Would appreciate someone more familiar with the isoseq ecosystem confirming whether that's the right approach here.

[SPPearce]

I have never heard of the tool, but I think that is the right thing to do. In theory we should deprecate the current module for a year and make a new one. https://nf-co.re/docs/developing/components/deprecating-components