feat: stub add flu workflow by d-callan · Pull Request #1222 · galaxyproject/brc-analytics

d-callan · 2026-04-03T03:51:23Z

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

Workflow Activation: Enabled flu workflow in YAML with ORGANISM scope and taxonomy ID 11320
Scope-based Architecture: Refactored ConfiguredValue types to support ASSEMBLY, ORGANISM, and SEQUENCE scopes
Feature Flag: Added flu workflow behind feature flag 'flu' for controlled rollout
Type Safety: Introduced proper type guards and discriminant properties for ConfiguredValue union types

Copilot

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_spec reference bundle.
Refactored Galaxy launch configuration types/logic to use a scope-discriminated ConfiguredValue union 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

getStaticPaths now generates pages for all workflows in catalog/output/workflows.json, including ones that the UI may hide behind feature flags (e.g. flu). Since WorkflowView/getWorkflow() doesn’t appear to enforce the flu flag, 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. in getStaticProps/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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Copilot · 2026-04-16T19:57:53Z

+                  "url": "https://zenodo.org/records/14628364/files/ref_1_pb2.fasta",
+                  "md5": "5c8e6c3e8f3a1c5e5e5e5e5e5e5e5e5e"
+                },
+                {
+                  "ext": "fasta",
+                  "src": "url",
+                  "url": "https://zenodo.org/records/14628364/files/ref_2_pb1.fasta",
+                  "md5": "5c8e6c3e8f3a1c5e5e5e5e5e5e5e5e5f"
+                },
+                {
+                  "ext": "fasta",
+                  "src": "url",
+                  "url": "https://zenodo.org/records/14628364/files/ref_3_pa.fasta",
+                  "md5": "5c8e6c3e8f3a1c5e5e5e5e5e5e5e5e60"
+                },
+                {
+                  "ext": "fasta",
+                  "src": "url",
+                  "url": "https://zenodo.org/records/14628364/files/ref_4_ha.fasta",
+                  "md5": "5c8e6c3e8f3a1c5e5e5e5e5e5e5e5e61"
+                },
+                {
+                  "ext": "fasta",
+                  "src": "url",
+                  "url": "https://zenodo.org/records/14628364/files/ref_5_np.fasta",
+                  "md5": "5c8e6c3e8f3a1c5e5e5e5e5e5e5e5e62"
+                },
+                {
+                  "ext": "fasta",
+                  "src": "url",
+                  "url": "https://zenodo.org/records/14628364/files/ref_6_na.fasta",
+                  "md5": "5c8e6c3e8f3a1c5e5e5e5e5e5e5e5e63"
+                },
+                {
+                  "ext": "fasta",
+                  "src": "url",
+                  "url": "https://zenodo.org/records/14628364/files/ref_7_mp.fasta",
+                  "md5": "5c8e6c3e8f3a1c5e5e5e5e5e5e5e5e64"
+                },
+                {
+                  "ext": "fasta",
+                  "src": "url",
+                  "url": "https://zenodo.org/records/14628364/files/ref_8_ns.fasta",
+                  "md5": "5c8e6c3e8f3a1c5e5e5e5e5e5e5e5e65"


The md5 values in this generated catalog/output/workflows.json entry don’t match the values defined in catalog/source/workflows.yml for the same Zenodo URLs (e.g. source has 0cc350... for ref_1_pb2.fasta, but output has 5c8e6c...). Since the app uses this output file to build the Galaxy collection_spec request (and will forward these hashes), mismatched checksums can cause integrity-check failures or misleading metadata. Regenerate catalog/output/workflows.json from source (or fix the build) so the emitted md5 values match the YAML.

Suggested change

"url": "https://zenodo.org/records/14628364/files/ref_1_pb2.fasta",

"md5": "5c8e6c3e8f3a1c5e5e5e5e5e5e5e5e5e"

},

{

"ext": "fasta",

"src": "url",

"url": "https://zenodo.org/records/14628364/files/ref_2_pb1.fasta",

"md5": "5c8e6c3e8f3a1c5e5e5e5e5e5e5e5e5f"

},

{

"ext": "fasta",

"src": "url",

"url": "https://zenodo.org/records/14628364/files/ref_3_pa.fasta",

"md5": "5c8e6c3e8f3a1c5e5e5e5e5e5e5e5e60"

},

{

"ext": "fasta",

"src": "url",

"url": "https://zenodo.org/records/14628364/files/ref_4_ha.fasta",

"md5": "5c8e6c3e8f3a1c5e5e5e5e5e5e5e5e61"

},

{

"ext": "fasta",

"src": "url",

"url": "https://zenodo.org/records/14628364/files/ref_5_np.fasta",

"md5": "5c8e6c3e8f3a1c5e5e5e5e5e5e5e5e62"

},

{

"ext": "fasta",

"src": "url",

"url": "https://zenodo.org/records/14628364/files/ref_6_na.fasta",

"md5": "5c8e6c3e8f3a1c5e5e5e5e5e5e5e5e63"

},

{

"ext": "fasta",

"src": "url",

"url": "https://zenodo.org/records/14628364/files/ref_7_mp.fasta",

"md5": "5c8e6c3e8f3a1c5e5e5e5e5e5e5e5e64"

},

{

"ext": "fasta",

"src": "url",

"url": "https://zenodo.org/records/14628364/files/ref_8_ns.fasta",

"md5": "5c8e6c3e8f3a1c5e5e5e5e5e5e5e5e65"

"url": "https://zenodo.org/records/14628364/files/ref_1_pb2.fasta"

},

{

"ext": "fasta",

"src": "url",

"url": "https://zenodo.org/records/14628364/files/ref_2_pb1.fasta"

},

{

"ext": "fasta",

"src": "url",

"url": "https://zenodo.org/records/14628364/files/ref_3_pa.fasta"

},

{

"ext": "fasta",

"src": "url",

"url": "https://zenodo.org/records/14628364/files/ref_4_ha.fasta"

},

{

"ext": "fasta",

"src": "url",

"url": "https://zenodo.org/records/14628364/files/ref_5_np.fasta"

},

{

"ext": "fasta",

"src": "url",

"url": "https://zenodo.org/records/14628364/files/ref_6_na.fasta"

},

{

"ext": "fasta",

"src": "url",

"url": "https://zenodo.org/records/14628364/files/ref_7_mp.fasta"

},

{

"ext": "fasta",

"src": "url",

"url": "https://zenodo.org/records/14628364/files/ref_8_ns.fasta"

Copilot · 2026-04-16T19:57:53Z

    readRunsPaired: readRunsPaired ?? null,
    readRunsSingle: readRunsSingle ?? null,
-    // referenceAssembly is currently always set, but there are workflows that don't require referenceAssembly.
-    // xref https://github.com/galaxyproject/brc-analytics/issues/652
    referenceAssembly: referenceAssembly!,
    sampleSheet: null,


referenceAssembly: referenceAssembly! can still be undefined at runtime because the validation above only checks ASSEMBLY_FASTA_URL, not ASSEMBLY_ID (and not all ASSEMBLY-scope workflows require ASSEMBLY_FASTA_URL). This can enable the launch button and then generate an invalid Galaxy landing request. Consider requiring referenceAssembly for all ASSEMBLY-scope workflows, or at least when the workflow has ASSEMBLY_ID in its parameters, and avoid the non-null assertion here.

Copilot · 2026-04-16T19:57:53Z

+      const result = getConfiguredValues(BASE_CONFIGURED_INPUT, workflow);
+
+      expect(result).toBeDefined();
+      expect(result?._scope).toBe("SEQUENCE");
+    });


The SEQUENCE-scope expectations here don't match getConfiguredValues: getSequenceScopeConfiguredValues returns undefined unless both configuredInput.sequence is non-empty and configuredInput.numberOfHits is defined. Since BASE_CONFIGURED_INPUT doesn't set either, these assertions (toBeDefined(), _scope === "SEQUENCE", and the default numberOfHits/sequence checks) will fail. Update the test to provide sequence + numberOfHits, or change the expectations to toBeUndefined() when they’re missing.

Copilot · 2026-04-16T19:57:54Z

+      const result = getConfiguredValues(BASE_CONFIGURED_INPUT, workflow);
+
+      expect(result?._scope).toBe("SEQUENCE");
+      // Type guard would narrow to SequenceConfiguredValue
+      if (result && result._scope === "SEQUENCE") {
+        expect(result.numberOfHits).toBe(10);
+      }


This SEQUENCE type-guard test calls getConfiguredValues(BASE_CONFIGURED_INPUT, workflow) but BASE_CONFIGURED_INPUT lacks sequence and numberOfHits, so getConfiguredValues should return undefined and the _scope assertions won’t hold. Provide valid SEQUENCE inputs (e.g., sequence + numberOfHits) before asserting _scope === "SEQUENCE" / numberOfHits.

d-callan added 4 commits April 2, 2026 23:33

feat: configure flu workflow and add to workflow json

621b24c

fix: build pages regardless of showcomingsoon workflow category flag

941a3d2

feat: simple stepper-less wiring of flu workflow into app

fa87a1e

feat: add tests for refactored getConfiguredValues

1b1a75d

github-project-automation bot added this to BRC development tasks Apr 3, 2026

github-actions bot added the feat label Apr 3, 2026

Merge branch 'main' into add-flu-workflow

7cd404c

d-callan assigned NoopDog Apr 9, 2026

Merge branch 'main' into add-flu-workflow

35127d2

NoopDog requested a review from Copilot April 16, 2026 19:47

Copilot started reviewing on behalf of NoopDog April 16, 2026 19:47 View session

Copilot AI reviewed Apr 16, 2026

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feat: stub add flu workflow#1222

feat: stub add flu workflow#1222
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d-callan commented Apr 3, 2026

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