Improve SDA output

Author: bbimber

singlecell/resources/chunks/RunSDA.R

@@ -16,6 +16,9 @@ sdaFiles <- data.frame(DatasetId = character(), FileName = character())
 
     sdaResults <- bindArgs(CellMembrane::RunSDA, seuratObj)()
 
+    outputFileId <- ifelse(datasetId %in% names(datasetIdToOutputFileId), yes = datasetIdToOutputFileId[[datasetId]], no = NA)
+    sdaResults$OutputFileId <- outputFileId
+
     fileName <- paste0('sda.', datasetId, '.rds')
     saveRDS(sdaResults, file = fileName)
 

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

@@ -1,6 +1,7 @@
 package org.labkey.singlecell.pipeline.singlecell;
 
 import au.com.bytecode.opencsv.CSVReader;
+import org.apache.commons.lang3.StringUtils;
 import org.json.old.JSONObject;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.reader.Readers;
@@ -127,6 +128,12 @@ else if (wrappers.size() > 1)
                 so.setReadset(wrapper.getReadsetId());
                 so.setName(wrapper.getDatasetName() == null ? wrapper.getDatasetId() : wrapper.getDatasetName() + ": SDA Analysis");
 
+                String jobDescription = StringUtils.trimToNull(ctx.getParams().optString("jobDescription"));
+                if (jobDescription != null)
+                {
+                    so.setDescription(jobDescription);
+                }
+
                 ctx.getFileManager().addSequenceOutput(so);
             }
         }