Include jobDescription in VCF output and bugfix library export

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java

@@ -677,8 +677,15 @@ private void processFile(File input, Integer libraryId, Integer readsetId, JobCo
                     so1.setCreated(new Date());
                     so1.setModified(new Date());
                     so1.setReadset(readsetId);
-                    so1.setDescription("Total samples: " + sampleCount);
+                    String description = "Total samples: " + sampleCount;
 
+                    String extraDescription = StringUtils.trimToNull(ctx.getParams().optString("jobDescription"));
+                    if (extraDescription != null)
+                    {
+                        description = description + '\n' + extraDescription;
+                    }
+
+                    so1.setDescription(description);
                     _resumer.getFileManager().addSequenceOutput(so1);
                 }
             }

singlecell/resources/web/singlecell/panel/LibraryExportPanel.js

@@ -676,7 +676,7 @@ Ext4.define('SingleCell.panel.LibraryExportPanel', {
                                 }
                                 else if (p[1] === 'HTO') {
                                     if (includeWithData || row['hashingReadsetId/totalFiles'] === 0) {
-                                        if (row['hashingReadsetId'] && row['hashingReadsetId/application'] && row['hashingReadsetId/application'].match('Cell Hashing')) {
+                                        if (row['hashingReadsetId'] && row['hashingReadsetId/application'] && row['hashingReadsetId/application'].match(/Cell Hashing/i)) {
                                             sortedRows.push(Ext4.apply({targetApplication: '10x HTO', laneAssignment: (p.length > 2 ? p[2] : null), plateAlias: (p.length > 3 ? p[3] : null)}, row));
                                             found = true;
                                             return false;
@@ -685,7 +685,7 @@ Ext4.define('SingleCell.panel.LibraryExportPanel', {
                                 }
                                 else if (p[1] === 'CITE') {
                                     if (includeWithData || row['citeseqReadsetId/totalFiles'] === 0) {
-                                        if (row['citeseqReadsetId'] && row['citeseqReadsetId/application'] && row['citeseqReadsetId/application'].match('CITE-Seq')) {
+                                        if (row['citeseqReadsetId'] && row['citeseqReadsetId/application'] && row['citeseqReadsetId/application'].match(/CITE-Seq/i)) {
                                             sortedRows.push(Ext4.apply({targetApplication: '10x CITE-Seq', laneAssignment: (p.length > 2 ? p[2] : null), plateAlias: (p.length > 3 ? p[3] : null)}, row));
                                             found = true;
                                             return false;