Update defaults for TCR and update repseqio dependencies

Author: bbimber

singlecell/resources/chunks/SeuratPrototype.R

@@ -71,7 +71,7 @@ for (datasetId in names(seuratObjects)) {
   if ('Saturation.RNA' %in% names(seuratObj@meta.data)) {
     meanSaturation.RNA <- mean(seuratObj$Saturation.RNA)
     if (!is.null(minSaturation) && meanSaturation.RNA < minSaturation) {
-      addErrorMessage(paste0('Mean RNA saturation was: ', meanSaturation.RNA, ' for dataset: ', datasetId, ', below threshold of: ', minSaturation))
+      addErrorMessage(paste0('Mean RNA saturation was: ', meanSaturation.RNA, ' for dataset: ', datasetId, ', below threshold of: ', minSaturation, ', total cells: ', ncol(seuratObj)))
     }
 
     metricData <- rbind(metricData, data.frame(dataId = datasetId, readsetId = datasetIdToReadset[[datasetId]], metricname = 'MeanSaturation.RNA', metricvalue = meanSaturation.RNA))

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

@@ -23,8 +23,8 @@ public Provider()
             super("AppendTcr", "Append TCR Data", "RDiscvr", "This uses Rdiscvr::DownloadAndAppendTcrClonotypes to append TCR data.", List.of(
                     SeuratToolParameter.create("allowMissing", "Allow Missing Data", "If checked, an error will be thrown if any sample lacks TCR data", "checkbox", new JSONObject()
                     {{
-                        put("checked", true);
-                    }}, true)
+                        put("checked", false);
+                    }}, false)
             ), null, null);
         }