12.12.23 UTAP: how to render the report.Rmd file to PDF

Change the the output header of report.Rmd file to the following (see example in the image below):

#output:
#html_document:
#includes:
#in_header: header.html
#toc: yes
#toc_depth: 3
#toc_float: no
#pdf_document:
#toc: yes
#toc_depth: '3'

output:
  pdf_document:
    latex_engine: pdflatex # Use pdflatex for the engine
    toc: yes
    toc_depth: 3
    keep_tex: true
self_contained: true
always_allow_html: true

run the following bash command:

singularity exec instance://utap bash -c "export PATH=$PATH:/opt/miniconda3/envs/utap/bin && export OPENSSL_CONF=/dev/null && /opt/miniconda3/envs/utap/bin/Rscript -e \"rmarkdown::render('<report.Rmd path>')\""

make sure to fill in the path to your Rmd file in the command above