Explicitly set job status to pass info message

Author: bbimber

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

@@ -6,6 +6,7 @@
 import org.apache.commons.lang3.math.NumberUtils;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
+import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.reader.Readers;
 import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
@@ -577,6 +578,7 @@ private void handlePossibleFailure(SequenceOutputHandler.JobContext ctx, String
                     ctx.getLogger().info("HTML not found: " + html.getPath());
                 }
 
+                ctx.getJob().setStatus(PipelineJob.TaskStatus.error, " Errors: " + StringUtils.join(errors, ";"));
                 throw new PipelineJobException(getProvider().getName() + " Errors: " + StringUtils.join(errors, ";"));
             }
             catch (IOException e)

singlecell/resources/chunks/RunSingleR.R

@@ -1,10 +1,6 @@
 for (datasetId in names(seuratObjects)) {
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
-    if (!is.na(Sys.getenv('SEQUENCEANALYSIS_MAX_THREADS', unset = NA))) {
-        nThreads <- Sys.getenv('SEQUENCEANALYSIS_MAX_THREADS')
-    }
-
     seuratObj <- bindArgs(CellMembrane::RunSingleR, seuratObj, disallowedArgNames = c('assay'))()
 
     saveData(seuratObj, datasetId)

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

@@ -22,7 +22,10 @@ public Provider()
             super("RunSingleR", "Run SingleR", "CellMembrane/SingleR", "This will run singleR on the input object(s), and save the results in metadata.", Arrays.asList(
                     SeuratToolParameter.create("showHeatmap", "Generate Heatmaps", "If checked, the SingleR heatmaps will be generated. These can be expensive for large datasets and are often less useful than the DimPlots, so skipping them sometimes makes sense.", "checkbox", new JSONObject(){{
 
-                    }}, false, "showHeatmap", true)
+                    }}, false, "showHeatmap", true),
+                    SeuratToolParameter.create("nThreads", "# Threads", "If provided, this value will be passed to BiocParallel::MulticoreParam().", "ldk-integerfield", new JSONObject(){{
+                        put("minValue", 0);
+                    }}, null)
             ), null, null);
         }