@@ -619,7 +619,7 @@ importCellRangerV2 <- function(

     if (is.null(cellRangerOutsV2)) {

         if (is.null(reference) | is.null(dataTypeV2)) {

             stop("'reference' and 'dataTypeV2' are required ",

-                 "when 'cellRangerOutsV2 is not specified!'")

+                 "when 'cellRangerOutsV2' is not specified!")

         }

     }

@@ -21,7 +21,8 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {

           cellRangerDirs = entry$params$cellRangerDirs,

           sampleDirs = entry$params$sampleDirs,

           sampleNames = entry$params$sampleNames,

-          delayedArray = delayedArray

+          delayedArray = delayedArray,

+          reference = entry$params$reference

         )

       }

@@ -131,7 +131,7 @@ importCRSDir <- function(failed = FALSE) {

     shinyFiles::shinyDirButton("sDirectory", label = "Choose Directory", title = "Upload"),

     # A UI to display what users select

     verbatimTextOutput("sDirectoryPath", placeholder = TRUE),

-

+    tags$div(id = "sDirTable"),

     h3("Sample Name"),

     h5("If you do not provide an alternate sample name, the sample name will be set to the sample directory name."),

     textInput("sSampleID", ""),

@@ -400,6 +400,24 @@ shinyServer(function(input, output, session) {

         # create a new table for the selected directory

         count <- 0

         if (!is.na(path)) {

+          # Add Reference selection for cellRangerV2

+          if (input$algoChoice == "cellRanger2") {

+            ## Identify available reference

+            firstSampleDir <- list.dirs(path, recursive = FALSE)[1]

+            refPath <- file.path(firstSampleDir, "outs/filtered_gene_bc_matrices")

+            refList <- basename(list.dirs(refPath, recursive = FALSE))

+            ## Add UI

+            insertUI(

+              selector = "#bDirTable",

+              ui = fluidRow(

+                column(

+                  6,

+                  selectInput("cr2_b_Ref", "Reference:", refList)

+                )

+              )

+            )

+          }

+          # Add Sample Rename rows

           counts <- vector()

           for (sample in list.dirs(path, recursive = FALSE)) {

             count <- count+1

@@ -438,6 +456,25 @@ shinyServer(function(input, output, session) {

         vol <- roots[[input$sDirectory$root]]

         dirPaths$sDirectory <- paste0(vol, paste(unlist(input$sDirectory$path[-1]),

                                                  collapse = .Platform$file.sep))

+        path <- dirPaths$sDirectory

+        if (!is.na(path)) {

+          if (input$algoChoice == "cellRanger2") {

+            ## Identify available reference

+            refPath <- file.path(path, "outs/filtered_gene_bc_matrices")

+            refList <- basename(list.dirs(refPath, recursive = FALSE))

+            ## Add UI

+            insertUI(

+              selector = "#sDirTable",

+              ui = fluidRow(

+                column(

+                  6,

+                  selectInput("cr2_s_Ref", "Reference:", refList)

+                )

+              )

+            )

+          }

+          updateTextInput(session, "sSampleID", value = basename(path))

+        }

       }

     }

   )

@@ -522,7 +559,11 @@ shinyServer(function(input, output, session) {

             name <- basename(sample)

           }

           id <- paste0("bnewSampleCR2", allImportEntries$id_count)

-          entry <- list(type="cellRanger2", id=id, params=list(cellRangerDirs = basePath, sampleDirs = basename(sample), sampleNames = name))

+          entry <- list(type="cellRanger2", id=id, 

+                        params=list(cellRangerDirs = basePath, 

+                                    sampleDirs = basename(sample), 

+                                    sampleNames = name,

+                                    reference = input$cr2_b_Ref))

           allImportEntries$samples <- c(allImportEntries$samples, list(entry))

           fluidRowStyle <- paste0(paste0("#", id), "{border-bottom: 1px solid #bababa; padding-top: .9%; padding-bottom: .5%}")

           removeBtnStyle <- paste0(paste0("#remove", id), "{padding-top: 0; padding-bottom: 0;}")

@@ -609,7 +650,11 @@ shinyServer(function(input, output, session) {

       # add the files to the appropriate reactiveValues

       if (input$algoChoice == "cellRanger2") {

         id <- paste0("snewSampleCR2", allImportEntries$id_count)

-        entry <- list(type="cellRanger2", id=id, params=list(cellRangerDirs = dirname(samplePath), sampleDirs = basename(samplePath), sampleNames = input$sSampleID))

+        entry <- list(type="cellRanger2", id=id, 

+                      params=list(cellRangerDirs = dirname(samplePath), 

+                                  sampleDirs = basename(samplePath), 

+                                  sampleNames = input$sSampleID,

+                                  reference = input$cr2_s_Ref))

         allImportEntries$samples <- c(allImportEntries$samples, list(entry))

         allImportEntries$id_count <- allImportEntries$id_count + 1

       } else {

@@ -647,7 +692,9 @@ shinyServer(function(input, output, session) {

     } else {

       if (input$algoChoice == "cellRanger2") {

         id <- paste0("dnewSampleCR2", allImportEntries$id_count)

-        entry <- list(type="cellRanger2", id=id, params=list(dataDir = dataPath, sampleName = input$dSampleID))

+        entry <- list(type="cellRanger2", id=id, 

+                      params=list(dataDir = dataPath, 

+                                  sampleName = input$dSampleID))

         allImportEntries$samples <- c(allImportEntries$samples, list(entry))

         allImportEntries$id_count <- allImportEntries$id_count + 1

       } else {