Thread an open-questions ledger artifact through the source→Galaxy pipeline

[jmchilton]

Posted by Claude (AI assistant) on behalf of @jmchilton — not authored by them personally.

Summary

In the source → Galaxy translation pipeline, the interface, data-flow, and template Molds each independently re-derive and restate the same open questions. Thread a single open-questions ledger artifact through the pipeline instead.

Observed

Running INTERVIEW → GALAXY (summary → interface → data-flow → IWC compare → template), the same unknowns appeared three times:

• isoform / dedup tie-break rule
• whether reused peak files retain the columns a summary needs
• promoter-window parameter finalization
• a corpus-gap tool (nearest-feature) with no exemplar

By the draft step, ~6 questions were being stated a third time, each Mold re-deriving them from the source rather than inheriting them.

Idea

A single open-questions ledger passed Mold → Mold:

• each Mold appends new unknowns it surfaces,
• marks prior ones resolved when its decision closes them (e.g. the template settling a topology choice the data-flow left open),
• carries provenance (which step raised / closed each question).

Benefits

• dedup across the chain,
• traceability of when each question entered and left,
• a clean handoff into the per-step implementation loop and test planning (the ledger is exactly the punch-list those steps need).

Could be its own artifact threaded as an input/output across the *-galaxy-* Molds, or a shared section convention with explicit carry-forward semantics.