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Pull request overview
Activates the Influenza consensus/subtyping workflow and extends the workflow-launch configuration model to support scope-based behavior (ASSEMBLY / ORGANISM / SEQUENCE), enabling a basic “Launch in Galaxy” flow while the stepper UI for non-assembly scopes is still pending.
Changes:
- Activated the influenza workflow in the workflow catalog (ORGANISM scope, taxonomy 11320) including a
collection_specreference bundle. - Refactored Galaxy launch configuration types/logic to use a scope-discriminated
ConfiguredValueunion and centralized landing URL selection. - Added feature-flag plumbing (
flu) and updated workflows listing logic to conditionally surface the flu workflow.
Reviewed changes
Copilot reviewed 13 out of 15 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/components/configureWorkflowInputs/getConfiguredValues.scope.test.ts | Adds tests for scope-based getConfiguredValues behavior. |
| pages/data/workflows/[trsId]/index.tsx | Adjusts static path generation for workflow pages. |
| pages/_app.tsx | Registers the flu feature flag. |
| catalog/source/workflows.yml | Activates influenza workflow; sets ORGANISM scope and adds collection_spec. |
| catalog/schema/generated/workflows.json | Updates generated schema description text. |
| catalog/schema/generated/schema.ts | Updates generated TS schema docstring for collection types. |
| catalog/py_package/catalog_build/generated_schema/schema.py | Updates generated Python schema docstring for collection types. |
| catalog/output/workflows.json | Adds influenza workflow entry to generated output catalog. |
| catalog/output/workflow-assembly-mappings.json | Adds influenza workflow to mapping output. |
| catalog/output/qc-report.workflow-mappings.md | Updates QC report totals and includes influenza workflow. |
| app/views/WorkflowsView/workflowsView.tsx | Threads flu feature flag into workflow listing computation. |
| app/views/WorkflowsView/utils.ts | Adds feature-flag-based inclusion of flu workflow in the listing. |
| app/components/.../UseLaunchGalaxy/utils.ts | Refactors getConfiguredValues to be scope-based and adds ORGANISM/SEQUENCE handlers. |
| app/components/.../UseLaunchGalaxy/useLaunchGalaxy.ts | Centralizes landing URL selection and adds type-guarded handling per workflow type. |
| app/components/.../UseLaunchGalaxy/types.ts | Introduces discriminated ConfiguredValue union + type guards. |
Comments suppressed due to low confidence (1)
pages/data/workflows/[trsId]/index.tsx:25
getStaticPathsnow generates pages for all workflows incatalog/output/workflows.json, including ones that the UI may hide behind feature flags (e.g. flu). SinceWorkflowView/getWorkflow()doesn’t appear to enforce thefluflag, this makes the flu workflow directly accessible via URL even when the flag is off, which undercuts the “controlled rollout” goal. Consider gating the workflow page itself (e.g. ingetStaticProps/client-side redirect) or excluding flagged workflows from static paths when the flag is disabled.
export const getStaticPaths: GetStaticPaths<Params> = async () => {
const paths = workflowCategories.reduce(
(acc, { workflows }) => {
for (const { trsId } of workflows) {
acc.push({ params: { trsId: formatTrsId(trsId) } });
}
return acc;
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hunterckx
requested changes
Apr 21, 2026
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hunterckx
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hunterckx
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A couple things that I think would be good to adjust before merging!
hunterckx
approved these changes
Apr 22, 2026
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Description
Activates the influenza consensus sequence and subtyping workflow, enabling direct launch in Galaxy with a basic "Launch in Galaxy" button. This PR does NOT include workflow stepper UI yet.
Changes