Flag more files for deletion

Author: bbimber

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

@@ -15,6 +15,7 @@
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
 import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.writer.PrintWriters;
 
 import java.io.BufferedReader;
@@ -50,6 +51,7 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra
         }
 
         ctx.getFileManager().addIntermediateFile(rmd);
+        ctx.getFileManager().addIntermediateFile(new File(rmd.getParentFile(), FileUtil.getBaseName(rmd.getName()) + "_files"));
 
         File markdownFile = getExpectedMarkdownFile(ctx, outputPrefix);
         if (!markdownFile.exists())

singlecell/resources/chunks/Functions.R

@@ -21,10 +21,7 @@ addIntermediateFile <- function(f) { intermediateFiles <<- c(intermediateFiles,
 # This will store any modified/transformed Seurat objects:
 newSeuratObjects <- list()
 
-print('Updating future.globals.maxSize')
-options(future.globals.maxSize = Inf)
-
-print(paste0('R memory: ', memory.limit()))
-print(paste0('R_MAX_VSIZE: ', Sys.getenv('R_MAX_VSIZE')))
+#print('Updating future.globals.maxSize')
+#options(future.globals.maxSize = Inf)
 
 options('Seurat.memsafe' = TRUE)

singlecell/src/org/labkey/singlecell/analysis/ProcessSingleCellHandler.java

@@ -389,11 +389,14 @@ else if (step.createsSeuratObjects())
                 throw new PipelineJobException(e);
             }
 
+            ctx.getJob().setStatus(PipelineJob.TaskStatus.running, "Creating Final HTML Report");
             File finalHtml = new File(ctx.getOutputDir(), "finalHtml.html");
             List<String> lines = new ArrayList<>();
             lines.add("rmarkdown::render(output_file = '" + finalHtml.getName() + "', input = '" + finalMarkdownFile.getName() + "', intermediates_dir  = '/work')");
             AbstractSingleCellPipelineStep.executeR(ctx, AbstractCellMembraneStep.CONTINAER_NAME, "pandoc", lines);
             _resumer.getFileManager().addIntermediateFile(finalMarkdownFile);
+            _resumer.getFileManager().addIntermediateFiles(_resumer.getMarkdownsInOrder());
+            _resumer.getFileManager().addIntermediateFiles(_resumer.getHtmlFilesInOrder());
 
             for (SingleCellStep.SeuratObjectWrapper output : currentFiles)
             {