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boutroslab · Jan 16, 2018 · 17483c2 · 17483c2
1 parent fd9ba07
commit 17483c2
Showing 1 changed file with 13 additions and 2 deletions.
diff --git a/source/app/extraction_server.r b/source/app/extraction_server.r
@@ -291,6 +291,9 @@ extractedFiles <- eventReactive(progress_fastq(), {
 
       }
       write(paste(userID, ": check if QC information for NGS files is present"), logFile, append = TRUE)
+      write(paste(userID, ": ", out), logFile, append = TRUE)
+      if("rqc" %in% names(out))
+      {
         if(out[["rqc"]] != "empty")
         {
           write(paste(userID, ": RQC information present"), logFile, append = TRUE)
@@ -303,6 +306,10 @@ extractedFiles <- eventReactive(progress_fastq(), {
           write(paste(userID, ": RQC information NOT present"), logFile, append = TRUE)
           out$rqc <- ""
         }
+      } else {
+        write(paste(userID, ": RQC information NOT present"), logFile, append = TRUE)
+        out$rqc <- ""
+      }
 
       shinyjs::enable("download_readcounts")
 
@@ -361,10 +368,11 @@ extractedFiles <- eventReactive(progress_fastq(), {
           # since mapping was done we have a large FASTQ file, which we want to delte for space purposes.
           # This is not done in case readcount files are uploaded, as wee need them later on.
           command <- "rm"
-          arguments <- file.path(userDir, out$oldpaths[i] ) 
-          system2(command, arguments)
+          arguments <- file.path(userDir, paste(i, ".seqFile", sep="") ) 
+          try(system2(command, arguments))
 
         }
+        write(paste(userID, ": extractedFiles Check Ratio"), logFile, append = TRUE)
         # check extractRatio
         if(file.access(file.path(paste(out$oldpaths[i],"_stats.txt", sep="")), mode = 4) == 0)
         {
@@ -377,6 +385,7 @@ extractedFiles <- eventReactive(progress_fastq(), {
         } else {
           out$extractRatio[[i]] <- NA
         }
+        write(paste(userID, ": extractedFiles Check Mapping"), logFile, append = TRUE)
 
         # check map match
         if(file.access(file.path(paste(out$oldpaths[i],"_map_stats.txt", sep="")), mode = 4) == 0)
@@ -423,6 +432,8 @@ extractedFiles <- eventReactive(progress_fastq(), {
       # save to userdir
       saveRDS(object = out, file = file.path(userDir, "extractedFiles.rds"))
 
+      write(paste(userID, ": extractedFiles saved"), logFile, append = TRUE)
+
       # SAM FILES
       command <- "rm"
       arguments <- file.path(userDir, "*.sam")