Support performCleanupAfterEachStep in more places of the UI

Author: bbimber

SequenceAnalysis/resources/web/SequenceAnalysis/panel/AlignmentImportPanel.js

@@ -94,6 +94,14 @@ Ext4.define('SequenceAnalysis.panel.AlignmentImportPanel', {
                 inputValue: true,
                 checked: true,
                 xtype: 'checkbox'
+            },{
+                fieldLabel: 'Perform Cleanup After Each Step',
+                helpPopup: 'Is selected, intermediate files from this job will be deleted after each step, instead of once at the end of the job. This can reduce the working directory size. Note: this will only apply if deleteIntermediateFiles is selected, and this is not supported across every possible pipeline type.',
+                name: 'performCleanupAfterEachStep',
+                inputValue: true,
+                uncheckedValue: false,
+                checked: true,
+                xtype: 'checkbox'
             },{
                 fieldLabel: 'Treatment of Input Files',
                 xtype: 'combo',

SequenceAnalysis/resources/web/SequenceAnalysis/panel/SequenceAnalysisPanel.js

@@ -309,6 +309,14 @@ Ext4.define('SequenceAnalysis.panel.SequenceAnalysisPanel', {
                 uncheckedValue: false,
                 checked: true,
                 xtype: 'checkbox'
+            },{
+                fieldLabel: 'Perform Cleanup After Each Step',
+                helpPopup: 'Is selected, intermediate files from this job will be deleted after each step, instead of once at the end of the job. This can reduce the working directory size. Note: this will only apply if deleteIntermediateFiles is selected, and this is not supported across every possible pipeline type.',
+                name: 'performCleanupAfterEachStep',
+                inputValue: true,
+                uncheckedValue: false,
+                checked: true,
+                xtype: 'checkbox'
             },{
                 fieldLabel: 'Copy Inputs To Working Directory?',
                 helpPopup: 'Check to copy the input files to the working directory.  Depending on your environment, this may or may not help performance.',

SequenceAnalysis/resources/web/SequenceAnalysis/panel/VariantProcessingPanel.js

@@ -74,6 +74,14 @@ Ext4.define('SequenceAnalysis.panel.VariantProcessingPanel', {
 				inputValue: true,
 				checked: true,
 				xtype: 'checkbox'
+			},{
+				fieldLabel: 'Perform Cleanup After Each Step',
+				helpPopup: 'Is selected, intermediate files from this job will be deleted after each step, instead of once at the end of the job. This can reduce the working directory size. Note: this will only apply if deleteIntermediateFiles is selected, and this is not supported across every possible pipeline type.',
+				name: 'performCleanupAfterEachStep',
+				inputValue: true,
+				uncheckedValue: false,
+				checked: true,
+				xtype: 'checkbox'
 			}, this.getSaveTemplateCfg()]
 		};
 	},

singlecell/resources/web/singlecell/panel/SingleCellProcessingPanel.js

@@ -97,6 +97,14 @@ Ext4.define('SingleCell.panel.SingleCellProcessingPanel', {
                 inputValue: true,
                 checked: true,
                 xtype: 'checkbox'
+            },{
+                fieldLabel: 'Perform Cleanup After Each Step',
+                helpPopup: 'Is selected, intermediate files from this job will be deleted after each step, instead of once at the end of the job. This can reduce the working directory size. Note: this will only apply if deleteIntermediateFiles is selected, and this is not supported across every possible pipeline type.',
+                name: 'performCleanupAfterEachStep',
+                inputValue: true,
+                uncheckedValue: false,
+                checked: true,
+                xtype: 'checkbox'
             }, this.getSaveTemplateCfg()]
         };
     },