Bugfix to nimble append arg parsing

bbimber · bbimber · commit 405cdafb9e31 · 2022-05-17T17:38:55.000-07:00
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/NimbleAppend.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/NimbleAppend.java
@@ -60,7 +60,7 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur
         ret.bodyLines.add("defaultLabKeyFolder <- '" + getPipelineCtx().getJob().getParameters().get("labkeyFolderPath") + "'");
 
         ret.bodyLines.add("nimbleGenomes <- list(");
-        String genomeStr = getPipelineCtx().getJob().getParameters().get("nimbleGenomes");
+        String genomeStr = getProvider().getParameterByName("nimbleGenomes").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class);
         JSONArray json = new JSONArray(genomeStr);
         for (int i = 0; i < json.length(); i++)
         {

Original file line number	Diff line number	Diff line change
`@@ -60,7 +60,7 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur`
`60`	`60`	`ret.bodyLines.add("defaultLabKeyFolder <- '" + getPipelineCtx().getJob().getParameters().get("labkeyFolderPath") + "'");`
`61`	`61`
`62`	`62`	`ret.bodyLines.add("nimbleGenomes <- list(");`
`63`		`- String genomeStr = getPipelineCtx().getJob().getParameters().get("nimbleGenomes");`
	`63`	`+ String genomeStr = getProvider().getParameterByName("nimbleGenomes").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class);`
`64`	`64`	`JSONArray json = new JSONArray(genomeStr);`
`65`	`65`	`for (int i = 0; i < json.length(); i++)`
`66`	`66`	`{`