I have a nextflow DSL2 workflow which uses an Rscript in one of the processes. However when running the workflow (on a HPC cluster), the .Rmd file is not found. I tried various ways of referring to the file/path.

The path to the .Rmd file is defined as a param in the config file.

params {
    rscript = "./myscript.Rmd"
}
process {
    withName: run_report {
        conda = './env_R.yml'
    }   
} 

Process like this:

  rscript = file(params.rscript)
  ...
   process run_report {
    ...
    input:
    ...
    path(rscript)
    output:
    ...
    script:
    """
    Rscript -e "rmarkdown::render("$rscript")"
    """
}

I also tried this, directly referencing the .Rmd file and a variation like Rscript -e "rmarkdown::render("./myscript.Rmd")"

   process run_report {     
        ...
        script:
        """
        Rscript -e "rmarkdown::render("myscript.Rmd")"
        """
    }

Env file

name: R_kn
channels: 
  - defaults
  - conda-forge
dependencies: 
  - r-base=4.2.2
  - r-rmarkdown