Ensure savedSeuratObjects.txt file has unique name per job

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 <- paste0('/work/" + getSavedSeuratFileName(outputPrefix) + "'");
 
         //Read RDS:
         body.add("");

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