Improve behavior on restart of single-cell processing jobs

bbimber · bbimber · commit b5d76986fe0f · 2022-11-07T09:46:59.000-08:00
diff --git a/singlecell/resources/chunks/Functions.R b/singlecell/resources/chunks/Functions.R
@@ -61,7 +61,9 @@ printName <- function(datasetId) {
 }
 
 savedFiles <- data.frame(datasetId = character(), datasetName = character(), filename = character(), outputFileId = character(), readsetId = character())
-write.table(savedFiles, file = 'savedSeuratObjects.txt', quote = FALSE, sep = '\t', row.names = FALSE, col.names = FALSE)
+if (file.exists('/work/savedSeuratObjects.txt')) {
+    unlink('/work/savedSeuratObjects.txt')
+}
 
 saveData <- function(seuratObj, datasetId) {
     print(paste0('Saving dataset: ', datasetId))

Original file line number	Diff line number	Diff line change
`@@ -61,7 +61,9 @@ printName <- function(datasetId) {`
`61`	`61`	`}`
`62`	`62`
`63`	`63`	`savedFiles <- data.frame(datasetId = character(), datasetName = character(), filename = character(), outputFileId = character(), readsetId = character())`
`64`		`-write.table(savedFiles, file = 'savedSeuratObjects.txt', quote = FALSE, sep = '\t', row.names = FALSE, col.names = FALSE)`
	`64`	`+if (file.exists('/work/savedSeuratObjects.txt')) {`
	`65`	`+ unlink('/work/savedSeuratObjects.txt')`
	`66`	`+}`
`65`	`67`
`66`	`68`	`saveData <- function(seuratObj, datasetId) {`
`67`	`69`	`print(paste0('Saving dataset: ', datasetId))`