@galaxyproject/orbit 0.0.0 → 0.9.0

package/extensions/orbit/vendor/skills/debug-galaxy-workflow-output/_provenance.json

@@ -0,0 +1,160 @@
+{
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+  "cast_target": "claude",
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+      "trigger": "When a failed workflow test has invocation failure, missing workflow outputs, cancelled/paused steps, subworkflow failures, or collection population errors.",
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+      "dst": "references/notes/iwc-shortcuts-anti-patterns.md",
+      "used_at": "runtime",
+      "load": "on-demand",
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+      "purpose": "Decide whether a proposed debug fix aligns with accepted IWC testing shortcuts or masks a real failure.",
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+      "dst": "references/notes/planemo-workflow-test-architecture.md",
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+      {
+        "id": "workflow-debug-report",
+        "kind": "markdown",
+        "default_filename": "workflow-debug-report.md",
+        "description": "Failure-surface classification with captured job/invocation/collection/assertion evidence and a recommended next step or reference-gap follow-up."
+      }
+    ],
+    "consumes": [
+      {
+        "id": "workflow-test-result",
+        "description": "Structured run handoff from run-workflow-test: Planemo result, invocation/job/artifact context, and the observed failure modality.",
+        "producers": [
+          "run-workflow-test"
+        ]
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+    ]
+  }
+}

package/extensions/orbit/vendor/skills/debug-galaxy-workflow-output/_verify.json

@@ -0,0 +1,4 @@
+{
+  "verify_schema_version": 1,
+  "entries": []
+}

package/extensions/orbit/vendor/skills/debug-galaxy-workflow-output/references/notes/galaxy-collection-semantics.md

@@ -0,0 +1,43 @@
+---
+type: research
+title: "Galaxy collection semantics"
+tags:
+  - target/galaxy
+status: draft
+created: 2026-04-30
+revised: 2026-05-05
+revision: 3
+license: MIT
+license_file: LICENSES/galaxy.LICENSE
+related_notes:
+  - "galaxy-xsd"
+  - "galaxy-collection-tools"
+  - "galaxy-apply-rules-dsl"
+  - "nextflow-to-galaxy-channel-shape-mapping"
+  - "nextflow-operators-to-galaxy-collection-recipes"
+  - "galaxy-tool-job-failure-reference"
+  - "galaxy-workflow-invocation-failure-reference"
+  - "iwc-transformations-survey"
+  - "galaxy-discover-datasets"
+sources:
+  - "https://github.com/galaxyproject/galaxy/blob/7765fae934fbfdee77e3be5f5b235e43735273ae/lib/galaxy/model/dataset_collections/types/collection_semantics.yml"
+companions:
+  - "galaxy-collection-semantics.yml"
+summary: "Vendored formal spec of Galaxy dataset-collection mapping/reduction semantics, with labeled examples and pinned test references."
+---
+
+> **Vendored from upstream**, pinned at SHA `7765fae`. One file travels with this note:
+>
+> - `galaxy-collection-semantics.yml` — the structured source. **Agents and casting should consume this.** It carries the `tests:` blocks that pin concrete Galaxy test names; the rendered upstream view drops them.
+>
+> The Foundry also vendors Galaxy's auto-generated MyST/LaTeX rendering of the same YAML, which
+> is what the human view below renders from. It is a site asset: casting does not carry it, so
+> do not look for it beside this note in a skill bundle. Sync is manual.
+>
+> **When to consult:** authoring or reasoning about Molds and patterns that touch `data_collection` inputs, map-over / reduction shape changes, sub-collection mapping, `paired_or_unpaired`, or `sample_sheet`.
+
+```vendored-myst
+file: galaxy-collection-semantics.upstream.myst
+source: https://github.com/galaxyproject/galaxy/blob/7765fae934fbfdee77e3be5f5b235e43735273ae/doc/source/dev/collection_semantics.md
+sha: 7765fae
+```