Workflow Semantics

Tracking issue: galaxyproject/galaxy#22200 — asks for an actionable workflow-semantics artifact modelled on collection_semantics.yml: prose → examples → concrete test references, so the workflow editor, workflow runtime, tool runtime, and CLI validation can all be checked against one source of truth. See also collection_semantics, the precedent this imitates.

Notes moved here 2026-08-25 from untracked markdown in the workflow_semantics galaxy worktree; progress is tracked in this vault from now on.

Where things stand

Current notes

• WORKFLOW_SEMANTICS_STATUS.md — the master document. Status capture, re-review of the original branch against dev, per-artifact verdicts, the recommended PR plan (PR-B..PR-F), the duplicate-detection results, and the open questions. Start here; everything else is input to it.
• workflow_semantics_facts.yml — the 140-record fact corpus (118 with a test: ref, 22 code-analysis-only). Byte-identical to the public gist linked from #22200. This is what PR-B seeds from — filtered to facts whose refs still resolve on dev, with line anchors replaced by symbol anchors (93% of line anchors rotted in five months; 0% of named-test refs did).
• SUBCOLLECTION_WHEN_REVIEW_STATE.md — mvdbeek’s 2026-08-26 review of #23369, the two branches it was split into, what was verified locally, and the seven open items.
• PR_UNCONDITIONAL_WHEN_VALUES_DESCRIPTION.md — description for the first half: the all-None collapse, the framework test, the unconditional docs. Branch subworkflow_mapping_per_step_semantics.
• PR_WHEN_ALIGNMENT_DESCRIPTION.md — description for the second half: the is_aligned_with guard, API + unit tests, conditional docs. Branch subworkflow_mapping_when_alignment, stacked on the first.
• WF_SEMANTICS_FACT_QUESTIONS.md — the Q1–Q21 question set plus §2’s extra fact records. Read with the status doc’s §3.8 corrections in hand: Q1, Q18 and Q19 are wrong, Q6 was the one genuinely unanswered question, and §2’s 15 - test: records duplicate lines 412–500 of the facts YAML.
• RESEARCH_GAPS_HIGH_PRIORITY.md — Q1 (job failure propagation), Q2 (pause step deps), Q14 (scheduling iteration state). Q1’s “Path 2” answer here is the highest-value known error; §3.8 has the corrected three-path account.
• RESEARCH_GAPS_MEDIUM_PRIORITY.md — Q12 (format_source), Q13 (timeout job cleanup), Q16 (nested error tracing), Q19 (job cache invalidation), Q20 (nested PJA substitution). Q19 is incomplete per §3.8.
• COMPONENT_GALAXY_WORKFLOW_EXPRESSION_CONTEXT.md — reference on how when / value_from expressions are evaluated (CWL JS via cwl_utils, cwlNodeEngine.js globals, Galaxy↔CWL type conversion).
• MAPPED_WORKFLOW_RECOVERY_PERFORMANCE.md — design exploration for avoiding repeated collection-tree matching and recursive child recovery on every scheduler pass by persisting compact output-axis lineage.

old_plans/

Superseded — kept for provenance, not for following.

• MEDIUM_PRIORITY_TEST_PLAN.md — 4 tests from the medium-priority gaps. Written, then mostly dropped or folded into existing fixtures by the duplicate-detection pass (status doc §5, PR-E).
• NULL_CHAIN_AND_MAPPING_COMBINATION_TESTS.md — test plan for Q4 (null propagation chains) and Q10 (subworkflow mapping combination). Same fate: Q10’s file survives as PR-D, the null-chain files fold into filter_null.gxwf.yml.
• SUBCOLLECTION_WHEN_PR_DESCRIPTION.md — the combined description as posted on #23369, before the split. Superseded by the two descriptions above.
• WHEN_SUBCOLLECTION_ISSUE.md — 2026-08-23 session handoff for the subworkflow/when collection-mapping bug. Superseded by PR #23369; its cited HEAD (950bd75e) is stale.