Skip configuration steps if we don't need them

Author: mvdbeek

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/PairedEndStep/pairedEndStep.tsx

@@ -17,8 +17,6 @@ export const PairedEndStep = ({
   entryLabel,
   index,
   onConfigure,
-  onLaunchGalaxy,
-  status,
 }: StepProps): JSX.Element => {
   const ena = useENA<ReadRun>();
   const table = useTable(ena.data);

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/hooks/UseLaunchGalaxy/useLaunchGalaxy.ts

@@ -13,7 +13,7 @@ export const useLaunchGalaxy = ({
   workflow,
 }: Props): UseLaunchGalaxy => {
   const { data: landingUrl, isLoading: loading, run } = useAsync<string>();
-  const configuredValue = getConfiguredValues(configuredInput);
+  const configuredValue = getConfiguredValues(configuredInput, workflow);
   const disabled = !configuredValue;
 
   const onLaunchGalaxy = useCallback(async (): Promise<void> => {

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/hooks/UseLaunchGalaxy/utils.ts

@@ -1,16 +1,41 @@
 import { ConfiguredInput } from "../../../../../../../../../../../../views/WorkflowInputsView/hooks/UseConfigureInputs/types";
+import { Workflow } from "../../../../../../../../../../../../apis/catalog/brc-analytics-catalog/common/entities";
+import { WORKFLOW_PARAMETER_VARIABLE } from "../../../../../../../../../../../../apis/catalog/brc-analytics-catalog/common/schema-entities";
 import { ConfiguredValue } from "./types";
 
 /**
  * Returns the configured values from the configured input.
  * @param configuredInput - Configured input.
+ * @param workflow - Workflow to check required parameters.
  * @returns Configured values.
  */
 export function getConfiguredValues(
-  configuredInput: ConfiguredInput
+  configuredInput: ConfiguredInput,
+  workflow: Workflow
 ): ConfiguredValue | undefined {
   const { geneModelUrl, readRuns, referenceAssembly } = configuredInput;
-  if (!geneModelUrl || !readRuns || !referenceAssembly) return;
+
+  // If workflow is not available yet, return undefined
+  if (!workflow?.parameters) return undefined;
+
+  // Check which parameters are required by the workflow
+  const requiresReference = workflow.parameters.some(
+    (param) => param.variable === WORKFLOW_PARAMETER_VARIABLE.ASSEMBLY_FASTA_URL
+  );
+  const requiresGTF = workflow.parameters.some(
+    (param) => param.variable === WORKFLOW_PARAMETER_VARIABLE.GENE_MODEL_URL
+  );
+  const requiresFASTQ = workflow.parameters.some(
+    (param) =>
+      param.variable === WORKFLOW_PARAMETER_VARIABLE.SANGER_READ_RUN_PAIRED ||
+      param.variable === WORKFLOW_PARAMETER_VARIABLE.SANGER_READ_RUN_SINGLE
+  );
+
+  // Only check for required values
+  if (requiresReference && !referenceAssembly) return;
+  if (requiresGTF && !geneModelUrl) return;
+  if (requiresFASTQ && !readRuns) return;
+
   return {
     geneModelUrl,
     readRuns,

app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/stepper.tsx

@@ -8,9 +8,19 @@ export const Stepper = ({ workflow, ...props }: Props): JSX.Element => {
   const requiresGTF = workflow.parameters.some(
     (param) => param.variable === WORKFLOW_PARAMETER_VARIABLE.GENE_MODEL_URL
   );
-  const steps = requiresGTF
-    ? STEPS
-    : STEPS.filter((step) => step.key !== "geneModelUrl");
+  const requiresFASTQ = workflow.parameters.some(
+    (param) =>
+      param.variable === WORKFLOW_PARAMETER_VARIABLE.SANGER_READ_RUN_PAIRED ||
+      param.variable === WORKFLOW_PARAMETER_VARIABLE.SANGER_READ_RUN_SINGLE
+  );
+
+  let steps = STEPS;
+  if (!requiresGTF) {
+    steps = steps.filter((step) => step.key !== "geneModelUrl");
+  }
+  if (!requiresFASTQ) {
+    steps = steps.filter((step) => step.key !== "readRuns");
+  }
   const { activeStep, onContinue, onEdit } = useStepper(steps);
   return (
     <StyledStepper activeStep={activeStep} {...STEPPER_PROPS}>