_bookdown.yml

book_filename: "thesis"
chapter_name: "Chapter "
rmd_files:
    - "index.Rmd"
    - "0-frontmatter/00-frontmatter.Rmd"
    - "1-introduction/00-introduction.Rmd"
    - "2-tools/00-tools.Rmd"
    - "3-simulation/00-simulation.Rmd"
    - "4-clustering-trees/00-clustering-trees.Rmd"
    - "5-analysis/00-analysis.Rmd"
    - "6-conclusion/00-conclusion.Rmd"
    - "9-references/00-references.Rmd"
    - "A1-splatter-additional/00-splatter-additional.Rmd"
    - "A2-splatter-docs/00-splatter-docs.Rmd"
    - "A3-simulation-comparison/00-simulation-comparison.Rmd"
    - "A4-clustree-docs/00-clustree-docs.Rmd"
    - "A5-organoid-publication/00-organoid-publication.Rmd"
    - "A6-analysis-methods/00-analysis-methods.Rmd"
    - "A7-session-info/00-session-info.Rmd"
download:
    - ["thesis.pdf", "PDF"]
    - ["thesis.docx", "Word"]
delete_merged_file: true
output_dir: "docs"