How can I run quarto_render with Rscript_call()

[lucygarner]

Hi,

I usually run Rmarkdown render with Rscript_call() as follows:

Rscript_call(
    rmarkdown::render,
     list(input = "Rscripts/1_make_seurat.rmd",
          output_format = "html_document",
          params = list(exp_name = exp),
          output_file = paste0("reports/", exp, "_make_seurat.html"))
)

I would like to do the same thing but with quarto_render(). I tried the following but it gave me an error:

Rscript_call(
    quarto_render,
    list(input = "Rscripts/1_make_seurat.qmd",
         output_format = "html_document",
         execute_params = list(exp_name = exp),
         output_file = paste0("reports/", exp, "_make_seurat.html"))
)

ERROR:

ERROR: Invalid format string
Error in `processx::run(quarto_bin, args, echo = TRUE)`:
! System command 'quarto' failed
---
Exit status: 1
stdout & stderr: <printed>
---
Backtrace:
 1. base::local({ …
 2. base::eval.parent(substitute(eval(quote(expr), envir)))
 3. base::eval(expr, p)
 4. base::eval(expr, p)
 5. base::eval(quote({ …
 6. base::eval(quote({ …
 7. base::do.call(f, x[[2]], envir = globalenv())
 8. (function (input = NULL, output_format = NULL, output_file = NULL, …
 9. processx::run(quarto_bin, args, echo = TRUE)
10. processx:::throw(new_process_error(res, call = sys.call(), echo = echo, …

[lucygarner]

I managed to fix this. It was an error in the output_format argument. For quarto, it should be "html" rather than "html_document".