code: def render_rmarkdown_file(filename):
      
      render_template = Template(
          'rmarkdown::render("$filename")'
      )
      render_string = render_template.substitute(
          filename=filename)
      report_dir = os.path.dirname(filename)
      rcmd = Rscript_cmd()
      with chdir(report_dir):
          do.run([rcmd, "--no-environ", "-e", render_string], "Rendering bcbioRNASeq quality control report.")
      return filename
docs: render a rmarkdown file using the rmarkdown library