Quarto + Shiny Automated Reporting: Passing Variables to a Separate PDF Report (.qmd)

I'm working on an automated reporting system using Quarto (flexdashboard) and Shiny. The idea is that users can upload data, interact with the dashboard to explore statistics, and then generate a PDF report that reflects their selected statistics.

Setup

My main Quarto file (main.qmd) is structured as a Shiny flexdashboard:

---
title: "Reporting Tool"
author: "XY"
output: flexdashboard::flex_dashboard
runtime: shiny
---

I have a separate Quarto file (pdf_file.qmd) that is responsible for generating the final PDF report. This file should receive selected input variables from the dashboard and render a report accordingly.

How I'm Calling the Report

In main.qmd, I trigger the report generation via downloadHandler:

output$download_report <- downloadHandler(
  filename = function() {
    paste0("microbiome-report-", Sys.Date(), ".pdf")
  },
  content = function(file) {
    # Ensure correct path resolution
    quarto_file <- normalizePath("src/pdf_file.qmd", mustWork = TRUE)
    temp_output_dir <- tempfile()
    dir.create(temp_output_dir, showWarnings = FALSE)

    tryCatch({
      # Render the Quarto report and specify output directory
      quarto::quarto_render(
        input = quarto_file,
        output_format = "pdf",
        output_file = "report.pdf",
        output_dir = temp_output_dir, 
        execute_params = list(
          physeq = isolate(reactive_phyloseq()),
          metadata = isolate(uploaded_metadata()),
          tax_level = isolate(input$tax_level),
          metadata_group = isolate(input$metadata_group),
          alpha_indices = isolate(input$alpha_indices)
        )
      )

      # Copy the generated file to the correct location for download
      file.copy(file.path(temp_output_dir, "report.pdf"), file, overwrite = TRUE)
      
    }, error = function(e) {
      print(paste("Error generating Quarto report:", e$message))
    })
  }  
)

The Problem

• When I try to download the report, Quarto cannot find pdf_file.qmd in the src/ folder.
• Running normalizePath("src/pdf_file.qmd", mustWork = TRUE) in R returns the correct absolute path, but Quarto still throws an error.
• The report does not generate, and I get:

  Warning: Error in normalizePath: path[1]="src/pdf_file.qmd": The system cannot find the specified path
  

What I Tried

• Verified that pdf_file.qmd exists in src/
• Used absolute paths in quarto_render()
• Tested quarto::quarto_render("src/pdf_file.qmd") manually (works fine outside Shiny)
• Ensured quarto::quarto_path() is correctly set up

Question

How can I properly call pdf_file.qmd from main.qmd in a Shiny + Quarto setup, ensuring that parameters are passed and the report generates correctly?