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