Add cleanup

Author: bbimber

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

@@ -42,6 +42,8 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra
         File rmd = createRmd(ctx, inputObjects, outputPrefix);
         executeR(ctx, rmd, outputPrefix);
 
+        ctx.getFileManager().addIntermediateFile(rmd);
+
         File markdownFile = getExpectedMarkdownFile(ctx, outputPrefix);
         if (!markdownFile.exists())
         {
@@ -269,6 +271,9 @@ public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerC
         SimpleScriptWrapper rWrapper = new SimpleScriptWrapper(ctx.getLogger());
         rWrapper.setWorkingDir(ctx.getOutputDir());
         rWrapper.execute(Arrays.asList("/bin/bash", localBashScript.getName()));
+
+        localRScript.delete();
+        localBashScript.delete();
     }
 
     protected String prepareValueForR(SeuratToolParameter pd)

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

@@ -267,6 +267,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                 {
                     throw new PipelineJobException("No seurat objects produced by: " + prepareRawCounts.getProvider().getName());
                 }
+                currentFiles.stream().map(SingleCellStep.SeuratObjectWrapper::getFile).forEach(_resumer.getFileManager()::addIntermediateFile);
 
                 _resumer.setStepComplete(0, action, output0.getSeuratObjects(), output0.getMarkdownFile(), output0.getHtmlFile());
             }
@@ -356,6 +357,9 @@ else if (step.createsSeuratObjects())
             for (File markdown : _resumer.getMarkdownsInOrder())
             {
                 finalMarkdown.chunks.add(new AbstractSingleCellPipelineStep.Chunk(null, null, null, Collections.emptyList(), "child='" + markdown.getName() + "'"));
+
+                //TODO: add markdown:
+                //_resumer.getFileManager().addIntermediateFile(markdown);
             }
             finalMarkdown.chunks.add(new AbstractSingleCellPipelineStep.SessionInfoChunk());