automatic barcode detection shiny

README.md

@@ -10,7 +10,7 @@ You can read more about zUMIs in our [paper](https://doi.org/10.1093/gigascience
 
 ## Changelog
 29 Mar 2019: [zUMIs2.4.0 released](https://github.com/sdparekh/zUMIs/releases/tag/zUMIs2.4.0).
-Improved stats to support protocols without UMIs. Creation of stats now also supports read group-chunking to reduce RAM usage. Rsubread::featureCounts multimapping settings were corrected. zUMIs does not create the intermediate "postmap" YAML file anymore - all options are stored in the user-provided YAML. zUMIs can now run RNA velocity for you (set option velocyto to "yes" in the YAML file). We assume velocyto is installed in path. Implemented a check for correct YAML formatting to prevent runs with bad config files.
+Improved stats to support protocols without UMIs. Creation of stats now also supports read group-chunking to reduce RAM usage. Rsubread::featureCounts multimapping settings were corrected. zUMIs does not create the intermediate "postmap" YAML file anymore - all options are stored in the user-provided YAML. zUMIs can now run RNA velocity for you (set option velocyto to "yes" in the YAML file). We assume velocyto is installed in path. Implemented a check for correct YAML formatting to prevent runs with bad config files. Barcode detection has been refined and now supports automatic detection by zUMIs guided by a whitelist of possible barcodes (eg. for 10xGenomics data). Thus we have introduced a new flag in the barcode section of the YAML file which controls the automatic barcode detection (eg. automatic: yes).  
 
 07 Feb 2019: [zUMIs2.3.0 released](https://github.com/sdparekh/zUMIs/releases/tag/zUMIs2.3.0).
 Implemented barcode binning according to specified hamming distance.

zUMIs-config_shiny.R

@@ -193,7 +193,7 @@ server <- function(input, output, session) {
   output$barcodeUI <- renderUI({
     switch(input$barcodeChoice,
            #"Automatic" = p(em("Intact barcodes will be detected automatically.")),
-           "Automatic" = textInput(inputId = "BCfile",label = "Optional: File to barcode whitelist to use for guiding automatic detection", value = "/fullpath/to/file.txt"),
+           "Automatic" = textInput(inputId = "BCfile",label = "Optional: File to barcode whitelist to use for guiding automatic detection", value = NULL),
            "Number of top Barcodes" = numericInput(inputId = "BCnum",label = "Number of barcodes to consider:",value = 100, min = 10, step = 1),
            "Barcode whitelist" = textInput(inputId = "BCfile",label = "File to barcode whitelist to use:", value = "/fullpath/to/file.txt")
     )
@@ -387,6 +387,7 @@ server <- function(input, output, session) {
       "barcodes" = list(
         "barcode_num" = input$BCnum,
         "barcode_file" = input$BCfile,
+        "automatic" = ifelse(input$barcodeChoice=="Automatic", "yes", "no"),
         "BarcodeBinning" = input$HamBC,
         "nReadsperCell" = input$nReadsBC
       ),
@@ -489,10 +490,11 @@ server <- function(input, output, session) {
       updateCheckboxInput(session = session, inputId = "doVelocity", value = ya$counting_opts$velocyto)
       updateCheckboxInput(session = session, inputId = "countPrimary", value = ya$counting_opts$primaryHit)
       updateCheckboxInput(session = session, inputId = "twoPass", value = ya$counting_opts$twoPass)
-      if (is.null(ya$barcodes$barcode_num) & is.null(ya$barcodes$barcode_file)) {
+      if (is.null(ya$barcodes$barcode_num) & ya$barcodes$automatic == "yes") {
         updateRadioButtons(session = session, inputId = "barcodeChoice", selected = "Automatic")
+        updateTextInput(session = session, inputId = "BCfile", value = ya$barcodes$barcode_file)
       }
-      if (!is.null(ya$barcodes$barcode_file)){
+      if (!is.null(ya$barcodes$barcode_file) & ya$barcodes$automatic == "no"){
         updateRadioButtons(session = session, inputId = "barcodeChoice", selected = "Barcode whitelist")
         updateTextInput(session = session, inputId = "BCfile", value = ya$barcodes$barcode_file)
       }

zUMIs-master.sh

@@ -3,7 +3,7 @@
 # Pipeline to run UMI-seq analysis from fastq to read count tables.
 # Authors: Swati Parekh, Christoph Ziegenhain, Beate Vieth & Ines Hellmann
 # Contact: [email protected] or [email protected]
-vers=2.4.0e
+vers=2.4.0f
 currentv=`curl -s https://raw.githubusercontent.com/sdparekh/zUMIs/master/zUMIs-master.sh | grep '^vers=' | cut -f2 -d "="`
 if [ "$currentv" != "$vers" ]; then echo -e "------------- \n\n Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs \n\n-------------"; fi