Unresolved Questions
Merged from Plans A, B, and C. Resolved items moved to individual plan docs.
Still Open
1. Round-Trip Utility Location
Does the round-trip utility live in galaxy-tool-util, gxformat2, or both? gxformat2 can’t depend on Galaxy, but galaxy-tool-util is runtime-independent.
Plans A, C — no user input yet
2. workflow_step Model Completeness
We don’t know if the workflow_step models are complete — we won’t know until we start validating real workflows. Expect to discover and fix gaps as we go.
Plans A, B, C — user confirmed this is expected; track as ongoing risk not a blocking question
3. __current_case__ in Reverse Pipeline
Assume omitting __current_case__ from format2-to-native conversion works fine. Validate via Galaxy framework tests and IWC corpus. Fixing any defects stemming from this is a project deliverable.
Plan C — user confirmed approach but wants validation as explicit deliverable
Resolved
| # | Question | Decision |
|---|---|---|
| 1 | Fill defaults or preserve only explicit? | Don’t fill. Native is fully filled; format2 may have absent defaults. |
| 2 | $link in format2 state? | workflow_step fails on $link. workflow_step_linked handles them. $link is frowned upon / not expected in real workflows. |
| 4 | Dynamic select validation? | Lenient pass-through when options unavailable. |
| 6 | Subworkflows: early or deferred? | Early phases — don’t get too far without support. |
| 7 | Toolshed lookup depth? | Full Tool Shed 2.0 API + local cache for reuse. |
| 8 | Unavailable tools? | Fail closed — report error. |
| 9 | Round-trip sweep: CI or local? | Part of workflow framework tests — all workflow tests exercise round-trip in CI. |