Improve pipeline logging

Author: bbimber

singlecell/resources/chunks/Functions.R

@@ -70,17 +70,16 @@ file.create(trackerFile)
 print(paste0('Total lines in ', trackerFile, ' on job start:', length(readLines(trackerFile))))
 
 saveData <- function(seuratObj, datasetId) {
-    message(paste0('Saving dataset: ', datasetId, ' with ', ncol(seuratObj), ' cells'))
+    logger::log_info(paste0('Saving dataset: ', datasetId, ' with ', ncol(seuratObj), ' cells'))
     print(paste0('Saving dataset: ', datasetId))
     print(seuratObj)
 
     seuratObj <- .TestSplitLayers(seuratObj)
 
     datasetIdForFile <- makeLegalFileName(datasetId)
     fn <- paste0(outputPrefix, '.', datasetIdForFile, '.seurat.rds')
-    message(paste0('Filename: ', fn))
 
-    message(paste0('Saving RDS file: ', fn, ' with ', ncol(seuratObj), ' cells'))
+    logger::log_info(paste0('Saving RDS file: ', fn, ' with ', ncol(seuratObj), ' cells'))
     barcodeFile <- paste0(outputPrefix, '.', datasetIdForFile, '.cellBarcodes.csv')
     metaFile <- paste0(outputPrefix, '.', datasetIdForFile, '.seurat.meta.txt')