Bugfix to nimble append

Author: bbimber

SequenceAnalysis/resources/web/SequenceAnalysis/field/GenomeField.js

@@ -8,6 +8,7 @@ Ext4.define('SequenceAnalysis.field.GenomeField', {
             displayField: 'name',
             valueField: 'rowid',
             queryMode: 'local',
+            triggerAction: 'all',
             store: {
                 type: 'labkey-store',
                 schemaName: 'sequenceanalysis',

singlecell/resources/web/singlecell/panel/NimbleAppendPanel.js

@@ -13,7 +13,7 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
             minWidth: 650,
 			border: true,
 			items: [{
-				html: 'This step will first run cellranger using the primary genome (selected above). The resulting BAM will be passed to nimble, which will align using each of the genomes selected below, creating supplemental feature counts. By default, the original cellranger output is discarded.',
+				html: 'This step will query nimble results for the selected genome(s). It will then append these results to the seurat object on the target assay.',
 				maxWidth: 600,
 				border: false,
 				style: 'padding-bottom: 10px;'
@@ -48,7 +48,7 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
 					header: 'Genome',
 					editor: this.genomeField,
 					renderer: function(val){
-						const store = this.up('singlecell-nimblealignpanel').genomeField.store
+						const store = this.up('singlecell-nimbleappendpanel').genomeField.store
 						if (val && store) {
 							const recIdx = store.find('rowid', val);
 							return store.getAt(recIdx).get('name');

singlecell/src/org/labkey/singlecell/run/NimbleAlignmentStep.java

@@ -32,7 +32,7 @@ public static class Provider extends AbstractAlignmentStepProvider<AlignmentStep
     {
         public Provider()
         {
-            super("Nimble", "This will run Nimble to generate a supplemental feature count matrix for the provided libraries", getCellRangerGexParams(getToolParameters()), new LinkedHashSet<>(PageFlowUtil.set("sequenceanalysis/field/GenomeFileSelectorField.js", "sequenceanalysis/field/GenomeField.js", "singlecell/panel/NimbleAlignPanel.js")), null, true, false, ALIGNMENT_MODE.MERGE_THEN_ALIGN);
+            super("Nimble", "This will run Nimble to generate a supplemental feature count matrix for the provided libraries", getCellRangerGexParams(getToolParameters()), new LinkedHashSet<>(PageFlowUtil.set("sequenceanalysis/field/GenomeField.js", "singlecell/panel/NimbleAlignPanel.js")), null, true, false, ALIGNMENT_MODE.MERGE_THEN_ALIGN);
         }
 
         @Override

singlecell/src/org/labkey/singlecell/run/NimbleAnalysis.java

@@ -29,7 +29,7 @@ public static class Provider extends AbstractAnalysisStepProvider<NimbleAnalysis
     {
         public Provider()
         {
-            super("NimbleAnalysis", "Nimble", null, "This will run Nimble to generate a supplemental feature count matrix for the provided libraries", NimbleAlignmentStep.getToolParameters(), new LinkedHashSet<>(PageFlowUtil.set("sequenceanalysis/field/GenomeFileSelectorField.js", "sequenceanalysis/field/GenomeField.js", "singlecell/panel/NimbleAlignPanel.js")), null);
+            super("NimbleAnalysis", "Nimble", null, "This will run Nimble to generate a supplemental feature count matrix for the provided libraries", NimbleAlignmentStep.getToolParameters(), new LinkedHashSet<>(PageFlowUtil.set("sequenceanalysis/field/GenomeField.js", "singlecell/panel/NimbleAlignPanel.js")), null);
         }
 
         @Override