diff --git a/app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/hooks/UseLaunchGalaxy/types.ts b/app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/hooks/UseLaunchGalaxy/types.ts
index 94348484c..271c567e3 100644
--- a/app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/hooks/UseLaunchGalaxy/types.ts
+++ b/app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/hooks/UseLaunchGalaxy/types.ts
@@ -8,21 +8,67 @@ import { UcscTrack } from "../../../../../../../../../../../../utils/ucsc-tracks
 import { COLUMN_TYPE } from "../../SampleSheetClassificationStep/types";
 import { Strandedness } from "../../StrandednessStep/types";
 
-export interface ConfiguredValue {
+// Base configured values shared across all scopes
+export interface BaseConfiguredValue {
+  readRunsPaired: EnaSequencingReads[] | null;
+  readRunsSingle: EnaSequencingReads[] | null;
+  tracks: UcscTrack[] | null;
+}
+
+// ASSEMBLY scope: workflows that operate on a specific genome assembly
+export interface AssemblyConfiguredValue extends BaseConfiguredValue {
+  _scope: "ASSEMBLY";
   designFormula: string | null;
   geneModelUrl: string | null;
-  numberOfHits?: number;
   primaryContrasts: PrimaryContrasts | null;
-  readRunsPaired: EnaSequencingReads[] | null;
-  readRunsSingle: EnaSequencingReads[] | null;
   referenceAssembly: string;
   sampleSheet: Record<string, string>[] | null;
   sampleSheetClassification: Record<string, COLUMN_TYPE | null> | null;
-  sequence?: string;
   strandedness: Strandedness | undefined;
-  tracks: UcscTrack[] | null;
 }
 
+// ORGANISM scope: workflows that operate at organism level (may not require specific assembly)
+// Organism scope workflows may have collection_spec (defined in workflow YAML) and variables.
+// fastaCollection can be either:
+// - User-selected assembly accessions (string[]) for user-defined FASTA collections
+// - Auto-configured via collection_spec in workflow YAML (handled by Galaxy API)
+export interface OrganismConfiguredValue extends BaseConfiguredValue {
+  _scope: "ORGANISM";
+  fastaCollection: string[] | null;
+}
+
+// SEQUENCE scope: workflows that operate on user-provided sequences
+export interface SequenceConfiguredValue extends BaseConfiguredValue {
+  _scope: "SEQUENCE";
+  numberOfHits?: number;
+  sequence?: string;
+}
+
+// Type guards for ConfiguredValue discrimination
+export function isAssemblyConfiguredValue(
+  value: ConfiguredValue
+): value is AssemblyConfiguredValue {
+  return value._scope === "ASSEMBLY";
+}
+
+export function isOrganismConfiguredValue(
+  value: ConfiguredValue
+): value is OrganismConfiguredValue {
+  return value._scope === "ORGANISM";
+}
+
+export function isSequenceConfiguredValue(
+  value: ConfiguredValue
+): value is SequenceConfiguredValue {
+  return value._scope === "SEQUENCE";
+}
+
+// Union type for all configured values
+export type ConfiguredValue =
+  | AssemblyConfiguredValue
+  | OrganismConfiguredValue
+  | SequenceConfiguredValue;
+
 export interface Status {
   disabled: boolean;
   error: string | null;
diff --git a/app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/hooks/UseLaunchGalaxy/useLaunchGalaxy.ts b/app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/hooks/UseLaunchGalaxy/useLaunchGalaxy.ts
index 2dd523971..719ce4272 100644
--- a/app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/hooks/UseLaunchGalaxy/useLaunchGalaxy.ts
+++ b/app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/hooks/UseLaunchGalaxy/useLaunchGalaxy.ts
@@ -11,9 +11,105 @@ import { CUSTOM_WORKFLOW } from "../../../../../../../../../../../../views/Analy
 import { DIFFERENTIAL_EXPRESSION_ANALYSIS } from "../../../../../../../../../../../../views/AnalyzeWorkflowsView/differentialExpressionAnalysis/constants";
 import { LEXICMAP } from "../../../../../../../../../../../../views/AnalyzeWorkflowsView/lexicmap/constants";
 import { LOGAN_SEARCH } from "../../../../../../../../../../../../views/AnalyzeWorkflowsView/loganSearch/constants";
-import { Props, UseLaunchGalaxy } from "./types";
+import { Workflow } from "../../../../../../../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
+import {
+  ConfiguredValue,
+  isAssemblyConfiguredValue,
+  isSequenceConfiguredValue,
+  Props,
+  UseLaunchGalaxy,
+} from "./types";
 import { getConfiguredValues, launchGalaxy } from "./utils";
 
+/**
+ * Gets the appropriate landing URL based on workflow type.
+ * @param workflow - Workflow to launch.
+ * @param configuredValue - Configured values for the workflow.
+ * @param origin - Origin URL for the Galaxy instance.
+ * @returns Promise resolving to the Galaxy workflow landing URL.
+ */
+async function getLandingUrlForWorkflow(
+  workflow: Workflow,
+  configuredValue: ConfiguredValue,
+  origin: string
+): Promise<string> {
+  if (workflow.trsId === CUSTOM_WORKFLOW.trsId) {
+    if (!isAssemblyConfiguredValue(configuredValue)) {
+      throw new Error("Invalid configured value for CUSTOM workflow");
+    }
+    return getDataLandingUrl(
+      configuredValue.referenceAssembly,
+      configuredValue.geneModelUrl,
+      configuredValue.readRunsSingle,
+      configuredValue.readRunsPaired,
+      null,
+      configuredValue.tracks,
+      origin
+    );
+  }
+
+  if (
+    workflow.trsId === LOGAN_SEARCH.trsId ||
+    workflow.trsId === LEXICMAP.trsId
+  ) {
+    if (!workflow.workflowId) {
+      throw new Error("Missing workflow ID for LMLS workflow");
+    }
+    if (
+      !isSequenceConfiguredValue(configuredValue) ||
+      !configuredValue.numberOfHits ||
+      !configuredValue.sequence
+    ) {
+      throw new Error("Missing required values for LMLS workflow");
+    }
+    return getLMLSLandingUrl(
+      workflow.workflowId,
+      configuredValue.numberOfHits,
+      configuredValue.sequence,
+      origin
+    );
+  }
+
+  if (workflow.trsId === DIFFERENTIAL_EXPRESSION_ANALYSIS.trsId) {
+    if (
+      !workflow.workflowId ||
+      !isAssemblyConfiguredValue(configuredValue) ||
+      !configuredValue.geneModelUrl ||
+      !configuredValue.sampleSheet ||
+      !configuredValue.sampleSheetClassification ||
+      !configuredValue.designFormula
+    ) {
+      throw new Error("Missing required values for DE workflow");
+    }
+    return getDeSeq2LandingUrl(
+      workflow.workflowId,
+      configuredValue.referenceAssembly,
+      configuredValue.geneModelUrl,
+      configuredValue.sampleSheet,
+      configuredValue.sampleSheetClassification,
+      configuredValue.designFormula,
+      configuredValue.primaryContrasts,
+      configuredValue.strandedness,
+      origin
+    );
+  }
+
+  return getWorkflowLandingUrl(
+    workflow.trsId,
+    isAssemblyConfiguredValue(configuredValue)
+      ? configuredValue.referenceAssembly
+      : "",
+    isAssemblyConfiguredValue(configuredValue)
+      ? configuredValue.geneModelUrl
+      : null,
+    configuredValue.readRunsSingle,
+    configuredValue.readRunsPaired,
+    null,
+    workflow.parameters,
+    origin
+  );
+}
+
 export const useLaunchGalaxy = ({
   configuredInput,
   workflow,
@@ -27,79 +123,14 @@ export const useLaunchGalaxy = ({
     if (!configuredValue) return;
     const origin = config.browserURL || window.location.origin;
 
-    let landingUrl = "";
-
-    if (workflow.trsId === CUSTOM_WORKFLOW.trsId) {
-      landingUrl = await run(
-        getDataLandingUrl(
-          configuredValue.referenceAssembly,
-          configuredValue.geneModelUrl,
-          configuredValue.readRunsSingle,
-          configuredValue.readRunsPaired,
-          null, // fastaCollection - not yet supported in UI
-          configuredValue.tracks,
-          origin
-        )
-      );
-    } else if (
-      workflow.trsId === LOGAN_SEARCH.trsId ||
-      workflow.trsId === LEXICMAP.trsId
-    ) {
-      // LMLS workflows use stored workflow IDs with sequence and numberOfHits parameters
-      if (!workflow.workflowId) {
-        throw new Error("Missing workflow ID for LMLS workflow");
-      }
-      landingUrl = await run(
-        getLMLSLandingUrl(
-          workflow.workflowId,
-          configuredValue.numberOfHits!,
-          configuredValue.sequence!,
-          origin
-        )
-      );
-    } else if (workflow.trsId === DIFFERENTIAL_EXPRESSION_ANALYSIS.trsId) {
-      if (
-        !workflow.workflowId ||
-        !configuredValue.geneModelUrl ||
-        !configuredValue.sampleSheet ||
-        !configuredValue.sampleSheetClassification ||
-        !configuredValue.designFormula
-      ) {
-        throw new Error("Missing required values for DE workflow");
-      }
-      landingUrl = await run(
-        getDeSeq2LandingUrl(
-          workflow.workflowId,
-          configuredValue.referenceAssembly,
-          configuredValue.geneModelUrl,
-          configuredValue.sampleSheet,
-          configuredValue.sampleSheetClassification,
-          configuredValue.designFormula,
-          configuredValue.primaryContrasts,
-          configuredValue.strandedness,
-          origin
-        )
-      );
-    } else {
-      landingUrl = await run(
-        getWorkflowLandingUrl(
-          workflow.trsId,
-          configuredValue.referenceAssembly,
-          configuredValue.geneModelUrl,
-          configuredValue.readRunsSingle,
-          configuredValue.readRunsPaired,
-          null, // fastaCollection - not yet supported in UI
-          workflow.parameters,
-          origin
-        )
-      );
-    }
+    const landingUrl = await run(
+      getLandingUrlForWorkflow(workflow, configuredValue, origin)
+    );
 
     if (!landingUrl) {
       throw new Error("Failed to retrieve Galaxy workflow launch URL.");
     }
 
-    // Launch the Galaxy workflow.
     launchGalaxy(landingUrl);
   }, [config, configuredValue, run, workflow]);
 
diff --git a/app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/hooks/UseLaunchGalaxy/utils.ts b/app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/hooks/UseLaunchGalaxy/utils.ts
index f8cfee59f..12bc1d61b 100644
--- a/app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/hooks/UseLaunchGalaxy/utils.ts
+++ b/app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/hooks/UseLaunchGalaxy/utils.ts
@@ -5,8 +5,6 @@ import {
 import { Workflow } from "../../../../../../../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
 import { WORKFLOW_PARAMETER_VARIABLE } from "../../../../../../../../../../../../apis/catalog/brc-analytics-catalog/common/schema-entities";
 import { DIFFERENTIAL_EXPRESSION_ANALYSIS } from "../../../../../../../../../../../../views/AnalyzeWorkflowsView/differentialExpressionAnalysis/constants";
-import { LEXICMAP } from "../../../../../../../../../../../../views/AnalyzeWorkflowsView/lexicmap/constants";
-import { LOGAN_SEARCH } from "../../../../../../../../../../../../views/AnalyzeWorkflowsView/loganSearch/constants";
 import { ConfiguredInput } from "../../../../../../../../../../../../views/WorkflowInputsView/hooks/UseConfigureInputs/types";
 import { ConfiguredValue } from "./types";
 
@@ -54,6 +52,7 @@ function getDEConfiguredValues(
   }
 
   return {
+    _scope: "ASSEMBLY",
     designFormula,
     geneModelUrl,
     primaryContrasts: primaryContrasts ?? null,
@@ -67,45 +66,13 @@ function getDEConfiguredValues(
   };
 }
 
-/**
- * Validates and returns configured values for SEQUENCE scope workflows.
- * SEQUENCE scope workflows (like LMLS) require sequence FASTA and numberOfHits from user input.
- * @param configuredInput - Configured input.
- * @returns Configured values for SEQUENCE workflow or undefined if invalid.
- */
-function getLMLSConfiguredValues(
-  configuredInput: ConfiguredInput
-): ConfiguredValue | undefined {
-  const { numberOfHits, sequence } = configuredInput;
-
-  // Validate required fields for LMLS workflow
-  if (!sequence || numberOfHits === undefined) {
-    return;
-  }
-
-  return {
-    designFormula: null,
-    geneModelUrl: null,
-    numberOfHits,
-    primaryContrasts: null,
-    readRunsPaired: null,
-    readRunsSingle: null,
-    referenceAssembly: "",
-    sampleSheet: null,
-    sampleSheetClassification: null,
-    sequence,
-    strandedness: undefined,
-    tracks: null,
-  };
-}
-
 /**
  * Validates and returns configured values for standard workflows.
  * @param configuredInput - Configured input.
  * @param workflow - Workflow to check required parameters.
- * @returns Configured values for standard workflow or undefined if invalid.
+ * @returns Configured values for ASSEMBLY workflow or undefined if invalid.
  */
-function getStandardConfiguredValues(
+function getAssemblyScopeConfiguredValues(
   configuredInput: ConfiguredInput,
   workflow: Workflow
 ): ConfiguredValue | undefined {
@@ -114,25 +81,25 @@ function getStandardConfiguredValues(
 
   // If workflow is not available yet, return undefined
   if (!workflow?.parameters) return;
+  // ASSEMBLY-scope workflows always require referenceAssembly
+  if (!referenceAssembly) return;
+
   // Check which parameters are required by the workflow
   const requiredParams = getRequiredParameterTypes(workflow);
 
-  // Only check for required values
-  if (requiredParams.ASSEMBLY_FASTA_URL && !referenceAssembly) return;
   // For geneModelUrl, treat empty string as valid (user skipped or will upload manually)
   if (requiredParams.GENE_MODEL_URL && geneModelUrl === null) return;
   if (requiredParams.SANGER_READ_RUN_SINGLE && !readRunsSingle) return;
   if (requiredParams.SANGER_READ_RUN_PAIRED && !readRunsPaired) return;
 
   return {
+    _scope: "ASSEMBLY",
     designFormula: null,
     geneModelUrl: geneModelUrl ?? null,
     primaryContrasts: null,
     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!,
+    referenceAssembly,
     sampleSheet: null,
     sampleSheetClassification: null,
     strandedness: undefined,
@@ -140,6 +107,52 @@ function getStandardConfiguredValues(
   };
 }
 
+/**
+ * Returns default configured values for ORGANISM scope workflows.
+ * ORGANISM scope workflows may have collection_spec and variables but don't require assembly-specific inputs.
+ * For Phase 1, return default/empty values to allow launching directly in Galaxy.
+ * The collection_spec will be automatically passed by the Galaxy API.
+ * Phase 2 will add stepper UI to populate these values from user input.
+ * @returns Configured values for ORGANISM workflow.
+ * (Phase 2): Add validation for required parameters (e.g., check if fastaCollection or
+ * other organism-specific inputs are required by the workflow and return undefined if missing).
+ */
+function getOrganismScopeConfiguredValues(): ConfiguredValue {
+  return {
+    _scope: "ORGANISM",
+    fastaCollection: null,
+    readRunsPaired: null,
+    readRunsSingle: null,
+    tracks: null,
+  };
+}
+
+/**
+ * Validates and returns configured values for SEQUENCE scope workflows.
+ * SEQUENCE scope workflows (like LMLS) require sequence FASTA and numberOfHits from user input.
+ * @param configuredInput - Configured input.
+ * @returns Configured values for SEQUENCE workflow or undefined if invalid.
+ */
+function getSequenceScopeConfiguredValues(
+  configuredInput: ConfiguredInput
+): ConfiguredValue | undefined {
+  const { numberOfHits, sequence } = configuredInput;
+
+  // Validate required fields for SEQUENCE workflows
+  if (!sequence || numberOfHits === undefined) {
+    return;
+  }
+
+  return {
+    _scope: "SEQUENCE",
+    numberOfHits,
+    readRunsPaired: null,
+    readRunsSingle: null,
+    sequence,
+    tracks: null,
+  };
+}
+
 /**
  * Returns the configured values from the configured input.
  * @param configuredInput - Configured input.
@@ -150,20 +163,20 @@ export function getConfiguredValues(
   configuredInput: ConfiguredInput,
   workflow: Workflow
 ): ConfiguredValue | undefined {
-  // Handle Differential Expression Analysis workflow separately
+  // Handle Differential Expression Analysis workflow separately (special case - not in IWC yet)
   if (workflow.trsId === DIFFERENTIAL_EXPRESSION_ANALYSIS.trsId) {
     return getDEConfiguredValues(configuredInput);
   }
 
-  // Handle LMLS workflows (SEQUENCE scope with no parameters)
-  if (
-    workflow.trsId === LOGAN_SEARCH.trsId ||
-    workflow.trsId === LEXICMAP.trsId
-  ) {
-    return getLMLSConfiguredValues(configuredInput);
+  // For all other workflows, use scope-based logic
+  switch (workflow.scope) {
+    case "ASSEMBLY":
+      return getAssemblyScopeConfiguredValues(configuredInput, workflow);
+    case "ORGANISM":
+      return getOrganismScopeConfiguredValues();
+    case "SEQUENCE":
+      return getSequenceScopeConfiguredValues(configuredInput);
   }
-
-  return getStandardConfiguredValues(configuredInput, workflow);
 }
 
 /**
diff --git a/app/views/WorkflowsView/utils.ts b/app/views/WorkflowsView/utils.ts
index d47e53689..a02fead72 100644
--- a/app/views/WorkflowsView/utils.ts
+++ b/app/views/WorkflowsView/utils.ts
@@ -56,18 +56,21 @@ function getTaxonomicLevelRealm(assembly: Assembly | undefined): string {
  * Filters out workflows that have no compatible assemblies for the current site.
  * Differential Expression Analysis is always included as an interim measure.
  * LMLS workflows (Logan Search and Lexicmap) are included when the 'lmls' feature flag is enabled.
+ * Flu workflow is conditionally included based on the 'flu' feature flag.
  * Each workflow includes the properties of the workflow itself along with the name of its category and the compatible assembly (if any).
  * @param workflowCategories - An array of workflow categories, each containing an array of workflows.
  * @param mappings - Workflow-assembly mappings for the current site.
  * @param organisms - Organisms.
  * @param isLmlsEnabled - Whether the 'lmls' feature flag is enabled.
+ * @param isFluEnabled - Whether the 'flu' feature flag is enabled.
  * @returns An array of workflows, where each workflow is a combination of a workflow and its category name.
  */
 export function getWorkflows(
   workflowCategories: WorkflowCategory[],
   mappings: WorkflowAssemblyMapping[],
   organisms: Organism[],
-  isLmlsEnabled = false
+  isLmlsEnabled = false,
+  isFluEnabled = false
 ): WorkflowEntity[] {
   const workflows: WorkflowEntity[] = [];
 
@@ -83,6 +86,15 @@ export function getWorkflows(
   for (const category of workflowCategories) {
     if (!category.workflows) continue;
     for (const workflow of category.workflows) {
+      const isFluWorkflow =
+        workflow.trsId ===
+        "#workflow/github.com/iwc-workflows/influenza-isolates-consensus-and-subtyping/main/versions/v0.3";
+
+      // Skip flu workflow if feature flag is disabled.
+      if (isFluWorkflow && !isFluEnabled) {
+        continue;
+      }
+
       // Skip workflows with no compatible assemblies.
       if (!workflowsWithAssemblies.has(workflow.trsId)) {
         continue;
diff --git a/app/views/WorkflowsView/workflowsView.tsx b/app/views/WorkflowsView/workflowsView.tsx
index 5a04dbef1..9c613b931 100644
--- a/app/views/WorkflowsView/workflowsView.tsx
+++ b/app/views/WorkflowsView/workflowsView.tsx
@@ -19,6 +19,7 @@ import { Organism } from "./types";
 export const WorkflowsView = (): JSX.Element => {
   const workflowCategories = getWorkflowCategories();
   const organisms = getOrganisms<Organism>();
+  const isFluEnabled = useFeatureFlag("flu");
   const isLmlsEnabled = useFeatureFlag("lmls");
   const [mappings, setMappings] = useState<WorkflowAssemblyMapping[] | null>(
     null
@@ -40,9 +41,15 @@ export const WorkflowsView = (): JSX.Element => {
   const workflows = useMemo(
     () =>
       mappings
-        ? getWorkflows(workflowCategories, mappings, organisms, isLmlsEnabled)
+        ? getWorkflows(
+            workflowCategories,
+            mappings,
+            organisms,
+            isLmlsEnabled,
+            isFluEnabled
+          )
         : [],
-    [isLmlsEnabled, mappings, organisms, workflowCategories]
+    [isFluEnabled, isLmlsEnabled, mappings, organisms, workflowCategories]
   );
 
   return <ExploreView data={workflows} Component={Workflows} />;
diff --git a/catalog/output/qc-report.workflow-mappings.md b/catalog/output/qc-report.workflow-mappings.md
index e61fd0e6e..7e718d0f5 100644
--- a/catalog/output/qc-report.workflow-mappings.md
+++ b/catalog/output/qc-report.workflow-mappings.md
@@ -27,6 +27,7 @@ None
 | Hi-C Processing: FASTQ to Balanced Cool Files | 4326 |
 | Hi-C Data Processing: FASTQ to Valid Interaction Pairs | 4326 |
 | Variant calling and consensus construction from paired end short read data of non-segmented viral genomes | 13 |
+| Influenza A isolate subtyping and consensus sequence generation | 7 |
 | Pox Virus Illumina Amplicon Workflow from half-genomes | 2 |
 | AMR Gene Detection | 393 |
 | Genome annotation with Braker3 | 4475 |
@@ -35,6 +36,6 @@ None
 
 ## Summary Statistics
 
-- Total active workflows: 24
-- Workflows with ≥1 compatible assembly: 24
+- Total active workflows: 25
+- Workflows with ≥1 compatible assembly: 25
 - Workflows with 0 compatible assemblies: 0
diff --git a/catalog/output/workflow-assembly-mappings.json b/catalog/output/workflow-assembly-mappings.json
index fb4413434..307abd39e 100644
--- a/catalog/output/workflow-assembly-mappings.json
+++ b/catalog/output/workflow-assembly-mappings.json
@@ -71,6 +71,10 @@
     "compatibleAssemblyCount": 4326,
     "workflowTrsId": "#workflow/github.com/iwc-workflows/hic-hicup-cooler/hic-fastq-to-pairs-hicup/versions/v0.3"
   },
+  {
+    "compatibleAssemblyCount": 7,
+    "workflowTrsId": "#workflow/github.com/iwc-workflows/influenza-isolates-consensus-and-subtyping/main/versions/v0.3"
+  },
   {
     "compatibleAssemblyCount": 2,
     "workflowTrsId": "#workflow/github.com/iwc-workflows/pox-virus-amplicon/main/versions/v0.4"
diff --git a/catalog/output/workflows.json b/catalog/output/workflows.json
index b5ee8e0b1..335278bb4 100644
--- a/catalog/output/workflows.json
+++ b/catalog/output/workflows.json
@@ -534,6 +534,78 @@
         "workflowDescription": "Variant calling and consensus sequence generation for batches of Illumina PE sequenced viruses with uncomplicated and stable genome structure (like e.g. Morbilliviruses).",
         "workflowName": "Variant calling and consensus construction from paired end short read data of non-segmented viral genomes"
       },
+      {
+        "iwcId": "influenza-isolates-consensus-and-subtyping-main",
+        "parameters": [
+          {
+            "key": "References per segment collection",
+            "collection_spec": {
+              "collection_type": "list",
+              "name": "Influenza A Segment References",
+              "elements": [
+                {
+                  "ext": "fasta",
+                  "md5": "0cc350480c0ef6d2583b4764adaabb5a",
+                  "src": "url",
+                  "url": "https://zenodo.org/records/14628364/files/ref_1_pb2.fasta"
+                },
+                {
+                  "ext": "fasta",
+                  "md5": "a8c9d6aa3c21ec24c42f480750dc4eca",
+                  "src": "url",
+                  "url": "https://zenodo.org/records/14628364/files/ref_2_pb1.fasta"
+                },
+                {
+                  "ext": "fasta",
+                  "md5": "a5f373e913c0f84ea00cba35ea81c703",
+                  "src": "url",
+                  "url": "https://zenodo.org/records/14628364/files/ref_3_pa.fasta"
+                },
+                {
+                  "ext": "fasta",
+                  "md5": "9476d2c02a0429e6b0e5a70ea2a94ef2",
+                  "src": "url",
+                  "url": "https://zenodo.org/records/14628364/files/ref_4_ha.fasta"
+                },
+                {
+                  "ext": "fasta",
+                  "md5": "3d0e28d72bba2c8b352d64052524473d",
+                  "src": "url",
+                  "url": "https://zenodo.org/records/14628364/files/ref_5_np.fasta"
+                },
+                {
+                  "ext": "fasta",
+                  "md5": "d8c21026a3defe01e020628e5b76227c",
+                  "src": "url",
+                  "url": "https://zenodo.org/records/14628364/files/ref_6_na.fasta"
+                },
+                {
+                  "ext": "fasta",
+                  "md5": "13b0b6900807d5e557348b0e69dc79ad",
+                  "src": "url",
+                  "url": "https://zenodo.org/records/14628364/files/ref_7_mp.fasta"
+                },
+                {
+                  "ext": "fasta",
+                  "md5": "e98fc11ed2c825e54d8d88b295449f41",
+                  "src": "url",
+                  "url": "https://zenodo.org/records/14628364/files/ref_8_ns.fasta"
+                }
+              ]
+            }
+          },
+          {
+            "key": "Sequenced paired-end data",
+            "variable": "SANGER_READ_RUN_PAIRED"
+          }
+        ],
+        "ploidy": "ANY",
+        "scope": "ORGANISM",
+        "taxonomyId": "11320",
+        "trsId": "#workflow/github.com/iwc-workflows/influenza-isolates-consensus-and-subtyping/main/versions/v0.3",
+        "workflowDescription": "This workflow performs subtyping and consensus sequence generation for batches of Illumina PE sequenced Influenza A isolates.",
+        "workflowName": "Influenza A isolate subtyping and consensus sequence generation"
+      },
       {
         "iwcId": "pox-virus-amplicon-main",
         "parameters": [
diff --git a/catalog/py_package/catalog_build/generated_schema/schema.py b/catalog/py_package/catalog_build/generated_schema/schema.py
index c862e0812..8eda83229 100644
--- a/catalog/py_package/catalog_build/generated_schema/schema.py
+++ b/catalog/py_package/catalog_build/generated_schema/schema.py
@@ -120,7 +120,7 @@ class WorkflowCategoryId(str, Enum):
 
 class CollectionType(str, Enum):
     """
-        Galaxy collection types supported for workflow parameters.
+        Galaxy collection types supported for collection_spec in workflow parameters.
     Currently only 'list' collections are supported, which represent a simple ordered list of datasets.
     """
 
diff --git a/catalog/schema/generated/schema.ts b/catalog/schema/generated/schema.ts
index f9c54baec..2b2dc5c6c 100644
--- a/catalog/schema/generated/schema.ts
+++ b/catalog/schema/generated/schema.ts
@@ -47,7 +47,7 @@ export enum WorkflowCategoryId {
     OTHER = "OTHER",
 };
 /**
-* Galaxy collection types supported for workflow parameters.
+* Galaxy collection types supported for collection_spec in workflow parameters.
 Currently only 'list' collections are supported, which represent a simple ordered list of datasets.
 */
 export enum CollectionType {
diff --git a/catalog/schema/generated/workflows.json b/catalog/schema/generated/workflows.json
index e6fe294d4..7f49f687c 100644
--- a/catalog/schema/generated/workflows.json
+++ b/catalog/schema/generated/workflows.json
@@ -13,7 +13,7 @@
             ]
         },
         "CollectionType": {
-            "description": "Galaxy collection types supported for workflow parameters.\nCurrently only 'list' collections are supported, which represent a simple ordered list of datasets.",
+            "description": "Galaxy collection types supported for collection_spec in workflow parameters.\nCurrently only 'list' collections are supported, which represent a simple ordered list of datasets.",
             "enum": [
                 "list"
             ],
diff --git a/catalog/source/workflows.yml b/catalog/source/workflows.yml
index d6ebad962..55aed9a5d 100644
--- a/catalog/source/workflows.yml
+++ b/catalog/source/workflows.yml
@@ -902,14 +902,53 @@ workflows:
       This workflow performs subtyping and consensus sequence generation
       for batches of Illumina PE sequenced Influenza A isolates.
     ploidy: ANY
+    scope: ORGANISM
+    taxonomy_id: 11320
     parameters:
       - key: References per segment collection
+        collection_spec:
+          collection_type: list
+          name: Influenza A Segment References
+          elements:
+            - ext: fasta
+              md5: 0cc350480c0ef6d2583b4764adaabb5a
+              src: url
+              url: https://zenodo.org/records/14628364/files/ref_1_pb2.fasta
+            - ext: fasta
+              md5: a8c9d6aa3c21ec24c42f480750dc4eca
+              src: url
+              url: https://zenodo.org/records/14628364/files/ref_2_pb1.fasta
+            - ext: fasta
+              md5: a5f373e913c0f84ea00cba35ea81c703
+              src: url
+              url: https://zenodo.org/records/14628364/files/ref_3_pa.fasta
+            - ext: fasta
+              md5: 9476d2c02a0429e6b0e5a70ea2a94ef2
+              src: url
+              url: https://zenodo.org/records/14628364/files/ref_4_ha.fasta
+            - ext: fasta
+              md5: 3d0e28d72bba2c8b352d64052524473d
+              src: url
+              url: https://zenodo.org/records/14628364/files/ref_5_np.fasta
+            - ext: fasta
+              md5: d8c21026a3defe01e020628e5b76227c
+              src: url
+              url: https://zenodo.org/records/14628364/files/ref_6_na.fasta
+            - ext: fasta
+              md5: 13b0b6900807d5e557348b0e69dc79ad
+              src: url
+              url: https://zenodo.org/records/14628364/files/ref_7_mp.fasta
+            - ext: fasta
+              md5: e98fc11ed2c825e54d8d88b295449f41
+              src: url
+              url: https://zenodo.org/records/14628364/files/ref_8_ns.fasta
         type_guide:
           class: Collection
       - key: Sequenced paired-end data
+        variable: SANGER_READ_RUN_PAIRED
         type_guide:
           class: Collection
-    active: false
+    active: true
     iwc_id: influenza-isolates-consensus-and-subtyping-main
   - trs_id: "#workflow/github.com/iwc-workflows/lncRNAs-annotation/main/versions/v0.1"
     categories:
diff --git a/pages/_app.tsx b/pages/_app.tsx
index c2fba459f..7e978b147 100644
--- a/pages/_app.tsx
+++ b/pages/_app.tsx
@@ -50,7 +50,7 @@ export type AppPropsWithComponent = AppProps & {
   pageProps: PageProps;
 };
 
-setFeatureFlags(["assistant", "lmls"]);
+setFeatureFlags(["assistant", "flu", "lmls"]);
 
 const queryClient = new QueryClient();
 
diff --git a/pages/data/workflows/[trsId]/index.tsx b/pages/data/workflows/[trsId]/index.tsx
index 86ca66af5..16a48a661 100644
--- a/pages/data/workflows/[trsId]/index.tsx
+++ b/pages/data/workflows/[trsId]/index.tsx
@@ -21,9 +21,7 @@ export interface Props {
 
 export const getStaticPaths: GetStaticPaths<Params> = async () => {
   const paths = workflowCategories.reduce(
-    (acc, { showComingSoon, workflows }) => {
-      // Special case, "showComingSoon", when false, should be skipped.
-      if (showComingSoon === false) return acc;
+    (acc, { workflows }) => {
       for (const { trsId } of workflows) {
         acc.push({ params: { trsId: formatTrsId(trsId) } });
       }
diff --git a/tests/components/configureWorkflowInputs/getConfiguredValues.scope.test.ts b/tests/components/configureWorkflowInputs/getConfiguredValues.scope.test.ts
new file mode 100644
index 000000000..dd4ef5030
--- /dev/null
+++ b/tests/components/configureWorkflowInputs/getConfiguredValues.scope.test.ts
@@ -0,0 +1,299 @@
+import type { Workflow } from "../../../app/apis/catalog/brc-analytics-catalog/common/entities";
+import {
+  WORKFLOW_PARAMETER_VARIABLE,
+  WORKFLOW_PLOIDY,
+  WORKFLOW_SCOPE,
+} from "../../../app/apis/catalog/brc-analytics-catalog/common/schema-entities";
+import { getConfiguredValues } from "../../../app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/hooks/UseLaunchGalaxy/utils";
+import type { ConfiguredInput } from "../../../app/views/WorkflowInputsView/hooks/UseConfigureInputs/types";
+
+// Mock workflow constants to avoid pulling in unneeded modules
+jest.mock(
+  "../../../app/views/AnalyzeWorkflowsView/differentialExpressionAnalysis/constants",
+  () => ({
+    DIFFERENTIAL_EXPRESSION_ANALYSIS: {
+      trsId: "differential-expression-analysis",
+    },
+  })
+);
+
+jest.mock(
+  "../../../app/views/AnalyzeWorkflowsView/loganSearch/constants",
+  () => ({
+    LOGAN_SEARCH: {
+      trsId: "logan-search",
+    },
+  })
+);
+
+jest.mock("../../../app/views/AnalyzeWorkflowsView/lexicmap/constants", () => ({
+  LEXICMAP: {
+    trsId: "lexicmap",
+  },
+}));
+
+describe("getConfiguredValues - scope-based logic", () => {
+  const BASE_WORKFLOW: Workflow = {
+    iwcId: "iwc-test",
+    parameters: [],
+    ploidy: WORKFLOW_PLOIDY.ANY,
+    scope: WORKFLOW_SCOPE.ASSEMBLY,
+    taxonomyId: null,
+    trsId: "#trs-test",
+    workflowDescription: "test workflow",
+    workflowName: "Test Workflow",
+  };
+
+  const BASE_CONFIGURED_INPUT: ConfiguredInput = {
+    designFormula: undefined,
+    geneModelUrl: null,
+    primaryContrasts: null,
+    readRunsPaired: null,
+    readRunsSingle: null,
+    referenceAssembly: undefined,
+    sampleSheet: undefined,
+    sampleSheetClassification: undefined,
+    strandedness: undefined,
+    tracks: null,
+  };
+
+  describe("ASSEMBLY scope", () => {
+    test("returns AssemblyConfiguredValue with _scope discriminant", () => {
+      const workflow: Workflow = {
+        ...BASE_WORKFLOW,
+        parameters: [],
+        scope: WORKFLOW_SCOPE.ASSEMBLY,
+      };
+
+      const configuredInput: ConfiguredInput = {
+        ...BASE_CONFIGURED_INPUT,
+        referenceAssembly: "GCF_000001405.40",
+      };
+
+      const result = getConfiguredValues(configuredInput, workflow);
+
+      expect(result).toBeDefined();
+      expect(result?._scope).toBe("ASSEMBLY");
+      expect(result).toHaveProperty("referenceAssembly", "GCF_000001405.40");
+    });
+
+    test("returns undefined when required ASSEMBLY_FASTA_URL param is missing", () => {
+      const workflow: Workflow = {
+        ...BASE_WORKFLOW,
+        parameters: [
+          {
+            key: "Reference genome",
+            variable: WORKFLOW_PARAMETER_VARIABLE.ASSEMBLY_FASTA_URL,
+          },
+        ],
+        scope: WORKFLOW_SCOPE.ASSEMBLY,
+      };
+
+      const configuredInput: ConfiguredInput = {
+        ...BASE_CONFIGURED_INPUT,
+        referenceAssembly: undefined, // Missing required value
+      };
+
+      const result = getConfiguredValues(configuredInput, workflow);
+
+      expect(result).toBeUndefined();
+    });
+
+    test("returns value when all required params are provided", () => {
+      const workflow: Workflow = {
+        ...BASE_WORKFLOW,
+        parameters: [
+          {
+            key: "Reference genome",
+            variable: WORKFLOW_PARAMETER_VARIABLE.ASSEMBLY_FASTA_URL,
+          },
+          {
+            key: "Gene model",
+            variable: WORKFLOW_PARAMETER_VARIABLE.GENE_MODEL_URL,
+          },
+        ],
+        scope: WORKFLOW_SCOPE.ASSEMBLY,
+      };
+
+      const configuredInput: ConfiguredInput = {
+        ...BASE_CONFIGURED_INPUT,
+        geneModelUrl: "https://example.com/genes.gff",
+        referenceAssembly: "GCF_000001405.40",
+      };
+
+      const result = getConfiguredValues(configuredInput, workflow);
+
+      expect(result).toBeDefined();
+      expect(result?._scope).toBe("ASSEMBLY");
+    });
+  });
+
+  describe("ORGANISM scope", () => {
+    test("returns OrganismConfiguredValue with _scope discriminant", () => {
+      const workflow: Workflow = {
+        ...BASE_WORKFLOW,
+        scope: WORKFLOW_SCOPE.ORGANISM,
+      };
+
+      const result = getConfiguredValues(BASE_CONFIGURED_INPUT, workflow);
+
+      expect(result).toBeDefined();
+      expect(result?._scope).toBe("ORGANISM");
+    });
+
+    test("returns OrganismConfiguredValue with fastaCollection property", () => {
+      const workflow: Workflow = {
+        ...BASE_WORKFLOW,
+        scope: WORKFLOW_SCOPE.ORGANISM,
+      };
+
+      const result = getConfiguredValues(BASE_CONFIGURED_INPUT, workflow);
+
+      expect(result).toBeDefined();
+      expect(result).toHaveProperty("fastaCollection", null);
+    });
+
+    test("always returns value regardless of configuredInput (no validation)", () => {
+      const workflow: Workflow = {
+        ...BASE_WORKFLOW,
+        scope: WORKFLOW_SCOPE.ORGANISM,
+      };
+
+      // Even with empty/null inputs, ORGANISM scope should return a value
+      const result = getConfiguredValues(BASE_CONFIGURED_INPUT, workflow);
+
+      expect(result).toBeDefined();
+    });
+  });
+
+  describe("SEQUENCE scope", () => {
+    test("returns SequenceConfiguredValue with _scope discriminant", () => {
+      const workflow: Workflow = {
+        ...BASE_WORKFLOW,
+        scope: WORKFLOW_SCOPE.SEQUENCE,
+      };
+
+      const configuredInput: ConfiguredInput = {
+        ...BASE_CONFIGURED_INPUT,
+        numberOfHits: 10,
+        sequence: ">test\nATCG",
+      };
+
+      const result = getConfiguredValues(configuredInput, workflow);
+
+      expect(result).toBeDefined();
+      expect(result?._scope).toBe("SEQUENCE");
+    });
+
+    test("returns SequenceConfiguredValue with numberOfHits and sequence", () => {
+      const workflow: Workflow = {
+        ...BASE_WORKFLOW,
+        scope: WORKFLOW_SCOPE.SEQUENCE,
+      };
+
+      const configuredInput: ConfiguredInput = {
+        ...BASE_CONFIGURED_INPUT,
+        numberOfHits: 10,
+        sequence: ">test\nATCG",
+      };
+
+      const result = getConfiguredValues(configuredInput, workflow);
+
+      expect(result).toBeDefined();
+      expect(result).toHaveProperty("numberOfHits", 10);
+      expect(result).toHaveProperty("sequence", ">test\nATCG");
+    });
+
+    test("returns undefined when required sequence is missing", () => {
+      const workflow: Workflow = {
+        ...BASE_WORKFLOW,
+        scope: WORKFLOW_SCOPE.SEQUENCE,
+      };
+
+      const configuredInput: ConfiguredInput = {
+        ...BASE_CONFIGURED_INPUT,
+        numberOfHits: 10,
+        // sequence is missing
+      };
+
+      const result = getConfiguredValues(configuredInput, workflow);
+
+      expect(result).toBeUndefined();
+    });
+
+    test("returns undefined when required numberOfHits is missing", () => {
+      const workflow: Workflow = {
+        ...BASE_WORKFLOW,
+        scope: WORKFLOW_SCOPE.SEQUENCE,
+      };
+
+      const configuredInput: ConfiguredInput = {
+        ...BASE_CONFIGURED_INPUT,
+        sequence: ">test\nATCG",
+        // numberOfHits is missing
+      };
+
+      const result = getConfiguredValues(configuredInput, workflow);
+
+      expect(result).toBeUndefined();
+    });
+  });
+
+  describe("type guards", () => {
+    test("ASSEMBLY scope value passes isAssemblyConfiguredValue", () => {
+      const workflow: Workflow = {
+        ...BASE_WORKFLOW,
+        scope: WORKFLOW_SCOPE.ASSEMBLY,
+      };
+
+      const configuredInput: ConfiguredInput = {
+        ...BASE_CONFIGURED_INPUT,
+        referenceAssembly: "GCF_000001405.40",
+      };
+
+      const result = getConfiguredValues(configuredInput, workflow);
+
+      expect(result?._scope).toBe("ASSEMBLY");
+      // Type guard would narrow to AssemblyConfiguredValue
+      if (result && result._scope === "ASSEMBLY") {
+        expect(result.referenceAssembly).toBe("GCF_000001405.40");
+      }
+    });
+
+    test("ORGANISM scope value passes isOrganismConfiguredValue", () => {
+      const workflow: Workflow = {
+        ...BASE_WORKFLOW,
+        scope: WORKFLOW_SCOPE.ORGANISM,
+      };
+
+      const result = getConfiguredValues(BASE_CONFIGURED_INPUT, workflow);
+
+      expect(result?._scope).toBe("ORGANISM");
+      // Type guard would narrow to OrganismConfiguredValue
+      if (result && result._scope === "ORGANISM") {
+        expect(result.fastaCollection).toBeNull();
+      }
+    });
+
+    test("SEQUENCE scope value passes isSequenceConfiguredValue", () => {
+      const workflow: Workflow = {
+        ...BASE_WORKFLOW,
+        scope: WORKFLOW_SCOPE.SEQUENCE,
+      };
+
+      const configuredInput: ConfiguredInput = {
+        ...BASE_CONFIGURED_INPUT,
+        numberOfHits: 10,
+        sequence: ">test\nATCG",
+      };
+
+      const result = getConfiguredValues(configuredInput, workflow);
+
+      expect(result?._scope).toBe("SEQUENCE");
+      // Type guard would narrow to SequenceConfiguredValue
+      if (result && result._scope === "SEQUENCE") {
+        expect(result.numberOfHits).toBe(10);
+      }
+    });
+  });
+});