Merge pull request #276 from BimberLab/24.3_fb_merge

Merge discvr-23.11 to discvr-24.3

Author: bbimber

singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java

@@ -43,12 +43,17 @@ public AbstractSingleCellPipelineStep(PipelineStepProvider<?> provider, Pipeline
         super(provider, ctx);
     }
 
+    private String getSavedSeuratFileName(String outputPrefix)
+    {
+        return outputPrefix + ".savedSeuratObjects.txt";
+    }
+
     @Override
     public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWrapper> inputObjects, String outputPrefix) throws PipelineJobException
     {
         SingleCellOutput output = new SingleCellOutput();
 
-        File tracker = new File(ctx.getOutputDir(), "savedSeuratObjects.txt");
+        File tracker = new File(ctx.getOutputDir(), getSavedSeuratFileName(outputPrefix));
         if (tracker.exists())
         {
             ctx.getLogger().debug("deleting pre-existing file: " + tracker.getName());
@@ -481,6 +486,7 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur
         }
         body.add("");
         body.add("outputPrefix <- '" + outputPrefix + "'");
+        body.add("trackerFile <- '/work/" + getSavedSeuratFileName(outputPrefix) + "'");
 
         //Read RDS:
         body.add("");

singlecell/resources/chunks/AvgExpression.R

@@ -32,7 +32,7 @@ GenerateAveragedData <- function(seuratObj, groupFields, addMetadata) {
         }
     }
 
-    a <- CellMembrane::PseudobulkSeurat(seuratObj, groupFields = groupFields, assays = assayName, additionalFieldsToAggregate = additionalFieldsToAggregate, nCountRnaStratification = nCountRnaStratification)
+    a <- CellMembrane::PseudobulkSeurat(seuratObj, groupFields = groupFields, assayToAggregate = assayName, additionalFieldsToAggregate = additionalFieldsToAggregate, nCountRnaStratification = nCountRnaStratification)
 
     if (addMetadata) {
         a <- Rdiscvr::QueryAndApplyMetadataUsingCDNA(a)

singlecell/resources/chunks/FindClustersAndDimRedux.R

@@ -2,7 +2,7 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- CellMembrane::FindClustersAndDimRedux(seuratObj, minDimsToUse = minDimsToUse)
+    seuratObj <- CellMembrane::FindClustersAndDimRedux(seuratObj, minDimsToUse = minDimsToUse, useLeiden = useLeiden)
 
     saveData(seuratObj, datasetId)
 

singlecell/resources/chunks/Functions.R

@@ -61,13 +61,13 @@ printName <- function(datasetId) {
 }
 
 savedFiles <- data.frame(datasetId = character(), datasetName = character(), filename = character(), outputFileId = character(), readsetId = character())
-if (file.exists('/work/savedSeuratObjects.txt')) {
-    print('Deleting pre-existing savedSeuratObjects.txt file')
-    unlink('/work/savedSeuratObjects.txt')
+if (file.exists(trackerFile)) {
+    print(paste0('Deleting pre-existing ', trackerFile, ' file'))
+    unlink(trackerFile)
 }
 
-file.create('/work/savedSeuratObjects.txt')
-print(paste0('Total lines in savedSeuratObjects.txt on job start:', length(readLines('savedSeuratObjects.txt'))))
+file.create(trackerFile)
+print(paste0('Total lines in ', trackerFile, ' on job start:', length(readLines(trackerFile))))
 
 saveData <- function(seuratObj, datasetId) {
     message(paste0('Saving dataset: ', datasetId, ' with ', ncol(seuratObj), ' cells'))
@@ -101,8 +101,9 @@ saveData <- function(seuratObj, datasetId) {
         stop('Error saving seurat objects, more than one row!')
     }
 
-    write.table(toAppend, file = 'savedSeuratObjects.txt', quote = FALSE, sep = '\t', row.names = FALSE, col.names = FALSE, append = TRUE)
-    print(paste0('Total lines in savedSeuratObjects.txt after save:', length(readLines('savedSeuratObjects.txt'))))
+    print(paste0('Total lines in ', trackerFile, ' before save:', length(readLines(trackerFile))))
+    write.table(toAppend, file = trackerFile, quote = FALSE, sep = '\t', row.names = FALSE, col.names = FALSE, append = TRUE)
+    print(paste0('Total lines in ', trackerFile, ' after save:', length(readLines(trackerFile))))
 
     # Write cell barcodes and metadata:
     metaDf <- seuratObj@meta.data

singlecell/resources/views/singleCellDataManagement.html

@@ -36,6 +36,9 @@
                     },{
                         name: 'VLoupe Files Needing TCR Import',
                         url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'sequenceanalysis', queryName: 'outputfiles', 'query.readset/status~isblank': null, 'query.readset/numTcrResults~eq': 0, 'query.category~eq': '10x VLoupe', 'query.sort': 'readset/name'})
+                    },{
+                        name: 'Stim Data Needing Activation Data',
+                        url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'sequenceanalysis', queryName: 'outputfiles', 'query.readset/assaytypes~contains': 'stim', 'query.readset/numTcrResults~eq': 0, 'query.category~eq': 'Seurat Object Prototype', 'query.readset/outputFileTypes~doesnotcontain': 'TCell Activation', 'query.sort': 'readset/name'})
                     },{
                         name: 'Loupe Files Missing Prototype',
                         url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'sequenceanalysis', queryName: 'outputfiles', 'query.category~eq': '10x Loupe File', 'query.readset/status~isblank': null, 'query.readset/cDNA/rowid~isnonblank': null, 'query.readset/outputFileTypes~doesnotcontain': 'Prototype', 'query.sort': 'readset/name', 'query.maxRows': 250})

singlecell/src/org/labkey/singlecell/pipeline/singlecell/CheckExpectations.java

@@ -34,7 +34,7 @@ public Provider()
                     SeuratToolParameter.create("requireSaturation", "Require Per-Cell Saturation", "If this dataset uses TCR sequencing, these data are required", "checkbox", null, true),
                     SeuratToolParameter.create("requireSingleR", "Require SingleR", "If checked, SingleR calls, including singleRConsensus are required to pass", "checkbox", null, true),
                     SeuratToolParameter.create("requireScGate", "Require scGate", "If checked, scGateConsensus calls are required to pass", "checkbox", null, true),
-                    SeuratToolParameter.create("requireRiraImmune", "Require RIRA Immune V2", "If checked, RIRA_Immune_v2 calls (field RIRA_Immune_v2.cellclass) are required to pass", "checkbox", null, true)
+                    SeuratToolParameter.create("requireRiraImmune", "Require RIRA Immune V2", "If checked, RIRA_Immune_v2 calls (field RIRA_Immune_v2.cellclass) are required to pass", "checkbox", null, false)
             ), null, null);
         }
 

singlecell/src/org/labkey/singlecell/pipeline/singlecell/FindClustersAndDimRedux.java

@@ -24,8 +24,10 @@ public Provider()
                     SeuratToolParameter.create("minDimsToUse", "Min. PCs to Use", "The minimum number of PCs to use", "ldk-integerfield", new JSONObject()
                     {{
                         put("minValue", 0);
-                    }}, 15)
+                    }}, 15),
+                    SeuratToolParameter.create("useLeiden", "Use Leiden Clustering", "If true, FindClusters() will use algorith=4 (leiden), as opposed to the default (louvain)", "checkbox", new JSONObject(){{
 
+                    }}, false)
             ), null, null);
         }