Rqc file format not detected or supported r shiny

Question

I want to upload a fastq file and render some plots using Rqc Package especially the rqcQA function.

This is the code :

library(shiny)
library(Rqc)
  ui <- fluidPage(
    titlePanel("Uploading Files"),
    sidebarLayout(
      sidebarPanel(
        fileInput('file1', 'Choose file to upload',
                  accept = c('.fastq')
        )
      ),
      mainPanel(
        plotOutput("plot1")
      )
    ))

  server <- function(input, output) {
      output$plot1 <- renderPlot({
        inFile <- input$file1
        if (is.null(inFile))
          return(NULL)
        # folder <- "D:/sample.fastq"
      rqcResultSet <- rqcQA(inFile$datapath, workers=1)
        rqcReadQualityBoxPlot(rqcResultSet)
      })
  }

  shinyApp(ui, server)

I got an error while reading the input :

'rqcQA' : Error in FUN(X[[i]], ...) : File format not detected or supported: 0

When i replace inFile$datapath by folder variable, i don't get any errors:

folder <- "D:/sample.fastq"
rqcResultSet <- rqcQA(folder, workers=1)

I did some research and i found the source code in Github, detectFileFormat.R is the file containing the function which specify the type format.

Any help will be appreciated.

Answer 1

The problem is that the file is renamed to 0 when you upload it to shiny and doesn't pass the rqcQA file tests. Try running:

file.rename(inFile$datapath,inFile$name)
rqcResultSet <- rqcQA(inFile$name,workers=1)

This just renames the file to the original name in the current wd.

You can alternatively do

rqcResultSet <- rqcQA(FastqFile(inFile$datapath))

to skip the file check.