Refactor: Deduplicate pseudo target rules (fast/meta/isolate)

[cmkobel]

Summary

The pseudo target rules fast, meta, and isolate in workflow/Snakefile (lines ~516–562) each define their own list of expand() calls for their outputs. Many of these expand calls are shared across targets — for example, annotation and QC outputs appear in all three.

Proposed approach

Build output lists from a shared base plus per-target additions. For example:

_base_outputs = [
    expand(...),  # annotation
    expand(...),  # QC
]

rule fast:
    input: _base_outputs

rule meta:
    input: _base_outputs + [expand(...)]  # + MAG-specific

rule isolate:
    input: _base_outputs + [expand(...)]  # + isolate-specific

This makes it clear what's shared vs. unique and prevents the lists from drifting out of sync.

Files to touch

• workflow/Snakefile (lines ~505–562)