Merge pull request #53 from LabKey/fb_merge_discvr-20.7

Merge discvr-20.7 to develop

Author: bbimber

.github/workflows/sync-repos.yml

@@ -1,5 +1,8 @@
 # Designed to keep develop branch as a perfect copy of LabKey fork
+name: Sync Repos
+
 on:
+  workflow_dispatch:
   schedule:
     - cron:  "10 */3 * * *"
 jobs:

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceAnalysisService.java

@@ -62,8 +62,6 @@ static public void setInstance(SequenceAnalysisService instance)
 
     abstract public void registerReadsetHandler(SequenceOutputHandler<SequenceOutputHandler.SequenceReadsetProcessor> handler);
 
-    //abstract public File createTabixIndex(File input, @Nullable Logger log) throws PipelineJobException;
-
     abstract public void registerDataProvider(SequenceDataProvider p);
 
     abstract public List<NavItem> getNavItems(Container c, User u, SequenceDataProvider.SequenceNavItemCategory category);
@@ -103,4 +101,6 @@ static public void setInstance(SequenceAnalysisService instance)
     abstract public String getScriptPath(String moduleName, String path) throws PipelineJobException;
 
     abstract public void sortGxf(Logger log, File input, @Nullable File output) throws PipelineJobException;
+
+    abstract public void ensureFeatureFileIndex(File input, Logger log) throws PipelineJobException;
 }

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequencePipelineService.java

@@ -125,5 +125,5 @@ static public void setInstance(SequencePipelineService instance)
 
     abstract public PreprocessingStep.Output simpleTrimFastqPair(File fq1, File fq2, List<String> params, File outDir, Logger log) throws PipelineJobException;
 
-    abstract public File runCiteSeqCount(PipelineStepOutput output, @Nullable String outputCategory, Readset htoReadset, File htoList, File cellBarcodeList, File outputDir, String basename, Logger log, List<String> extraArgs, boolean doHtoFiltering, @Nullable Integer minCountPerCell, File localPipelineDir, @Nullable Integer editDistance, boolean scanEditDistances, Readset parentReadset, @Nullable Integer genomeId, boolean generateHtoCalls) throws PipelineJobException;
+    abstract public File runCiteSeqCount(PipelineStepOutput output, @Nullable String outputCategory, Readset htoReadset, File htoList, File cellBarcodeList, File outputDir, String basename, Logger log, List<String> extraArgs, boolean doHtoFiltering, @Nullable Integer minCountPerCell, File localPipelineDir, @Nullable Integer editDistance, boolean scanEditDistances, Readset parentReadset, @Nullable Integer genomeId, boolean generateHtoCalls, boolean createOutputFiles) throws PipelineJobException;
 }

SequenceAnalysis/resources/external/scRNAseq/htoClassifier.Rmd

@@ -48,4 +48,13 @@ if (nrow(barcodeData) > 0 && ncol(barcodeData) > 0){
     }
 }
 
-```
+```
+
+## Print Session Info
+
+```{r SessionInfo}
+
+sessionInfo()
+
+```
+

SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.321-12.322.sql

@@ -0,0 +1 @@
+SELECT core.executeJavaUpgradeCode('updateBarcodeRC');

SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.321-12.322.sql

@@ -0,0 +1 @@
+EXEC core.executeJavaUpgradeCode 'updateBarcodeRC';

SequenceAnalysis/resources/views/illuminaSampleSheetExport.html

@@ -14,7 +14,7 @@
              LABKEY.Filter.create('rowid', pks.join(';'), LABKEY.Filter.Types.EQUALS_ONE_OF)
          ],
          sort: 'rowid,barcode5,barcode3',
-         columns: 'rowid,name,barcode5,barcode3,barcode5/sequence,barcode3/sequence,platform,sampleid',
+         columns: 'rowid,name,barcode5,barcode3,barcode5/sequence,barcode5/reverse_complement,barcode3/sequence,platform,sampleid',
          scope: this,
          success: function(result){
              if(result && result.rows.length){

SequenceAnalysis/resources/web/SequenceAnalysis/panel/IlluminaSampleExportPanel.js

@@ -604,7 +604,7 @@ Ext4.define('SequenceAnalysis.panel.IlluminaSampleExportPanel', {
             ['Sample_Well', ''],
             ['Sample_Project', ''],
             ['I7_Index_ID', 'barcode5'],
-            ['index', 'barcode5/sequence'],
+            ['index', 'barcode5/reverse_complement'],
             ['I5_Index_ID', 'barcode3'],
             ['index2', 'barcode3/sequence'],
             ['Description', ''],

SequenceAnalysis/resources/web/SequenceAnalysis/panel/SequenceImportPanel.js

@@ -472,7 +472,7 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
                     m.set('fileRecord1', rec.get('id'));
                     var fileArr = rec.get('fileName').replace(/\.gz$/, '').split('.');
                     fileArr.pop();
-                    var fileGroupId = fileArr.length == 1 ? fileArr[0] : fileArr.join('.');
+                    var fileGroupId = fileArr.length === 1 ? fileArr[0] : fileArr.join('.');
                     m.set('fileGroupId', fileGroupId);
                     //m.set('platformUnit', fileGroupId);
 
@@ -607,6 +607,7 @@ Ext4.define('SequenceAnalysis.panel.SequenceImportPanel', {
         map[sample] = map[sample] || {};
         map[sample][setId] = map[sample][setId] || [];
 
+        //NOTE: this likely will be a string
         if (readSet == 1){
             var m = Ext4.create('SequenceAnalysis.model.ReadsetDataModel', {});
             m.set('fileRecord1', rec.get('id'));

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

@@ -218,7 +218,14 @@ Ext4.define('SequenceAnalysis.panel.VariantProcessingPanel', {
                 commandLineParam: '--max_alternate_alleles',
                 defaultValue: 12
             },{
-                fieldXtype: 'checkbox',
+				fieldXtype: 'checkbox',
+				name: 'sharedPosixOptimizations',
+				label: 'Use Shared Posix Optimizations',
+				description: 'This enabled optimizations for large shared filesystems, such as lustre.',
+				commandLineParam: '--genomicsdb-shared-posixfs-optimizations',
+				defaultValue: true
+			},{
+            	fieldXtype: 'checkbox',
                 name: 'includeNonVariantSites',
                 label: 'Include Non-Variant Sites',
                 description: 'If checked, all sites will be output into the VCF, instead of just those where variants are detected.  This can dramatically increase the size of the VCF.',