Drop fasterq-dump argument

bbimber · bbimber · commit a7cdde084b9a · 2022-01-28T17:44:18.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java
@@ -249,7 +249,6 @@ public Pair<File, File> downloadSra(String dataset, File outDir) throws Pipeline
             args.add(SequencePipelineService.get().getJavaTempDir());
 
             args.add("-f"); //force-overwrite
-            args.add("--quiet");
 
             args.add("-O");
             args.add(outDir.getPath());
diff --git a/singlecell/resources/chunks/PrepareRawCounts.R b/singlecell/resources/chunks/PrepareRawCounts.R
@@ -5,7 +5,7 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- CellMembrane::ReadAndFilter10xData(dataDir = rawCountDir, datasetId = datasetId, datasetName = datasetName, emptyDropsLower = emptyDropsLower, emptyDropsFdrThreshold = emptyDropsFdrThreshold, useEmptyDropsCellRanger = useEmptyDropsCellRanger, nExpectedCells = nExpectedCells)
 
     if (!is.null(maxAllowableCells) && ncol(seuratObj) > maxAllowableCells) {
-        stop(paste0('The seurat object has more than the max allowable cells. Please review emptyDrops results'))
+        stop(paste0('The seurat object has ', ncol(seuratObj), ' cells, which is more than the max allowable cells (', maxAllowableCells, '). Please review emptyDrops results as this probably means thresholds were suboptimal.'))
     }
 
     saveData(seuratObj, datasetId)

Original file line number	Diff line number	Diff line change
`@@ -5,7 +5,7 @@ for (datasetId in names(seuratObjects)) {`
`5`	`5`	`seuratObj <- CellMembrane::ReadAndFilter10xData(dataDir = rawCountDir, datasetId = datasetId, datasetName = datasetName, emptyDropsLower = emptyDropsLower, emptyDropsFdrThreshold = emptyDropsFdrThreshold, useEmptyDropsCellRanger = useEmptyDropsCellRanger, nExpectedCells = nExpectedCells)`
`6`	`6`
`7`	`7`	`if (!is.null(maxAllowableCells) && ncol(seuratObj) > maxAllowableCells) {`
`8`		`- stop(paste0('The seurat object has more than the max allowable cells. Please review emptyDrops results'))`
	`8`	`+ stop(paste0('The seurat object has ', ncol(seuratObj), ' cells, which is more than the max allowable cells (', maxAllowableCells, '). Please review emptyDrops results as this probably means thresholds were suboptimal.'))`
`9`	`9`	`}`
`10`	`10`
`11`	`11`	`saveData(seuratObj, datasetId)`