SPAAM-community · jfy133 · Nov 25, 2025 · May 6, 2025 · May 14, 2025 · May 20, 2025
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -1,7 +1,8 @@
 on:
   workflow_dispatch:
   push:
-    branches: main
+    branches:
+      - main
 
 name: Quarto Publish
 

diff --git a/README.md b/README.md
@@ -52,10 +52,10 @@ If adding a new section chapter:
    - Do not place in `docs/assets/images/chapters/`!
 5. References in BibTex for the chapter should go a `references.bib` file into `assets/references/chapters/<chapter>`
 6. Add the `.qmd` file to the `_quarto.yml` config file in the `chapters:` scope
-7. Render the book the extensions' `Quarto: Render Book` command, or run the following
+7. Render the book the extensions' `Quarto: Render Book` command, or run the following while inside the reposiroty directory
 
    ```bash
-   quarto preview intro-to-ancient-metagenomics-book/ --render all --no-browser --no-watch-inputs
+   quarto preview . --render all --no-browser --no-watch-inputs
    ```
 
 8. Commit, push to GitHub, and open a PR against the `main` branch [^2]

diff --git a/_quarto.yml b/_quarto.yml
@@ -5,6 +5,24 @@ project:
 toc: true
 number-sections: true
 
+bibliography:
+  - assets/references/accessing-ancient-metagenomic-data.bib
+  - assets/references/ancient-metagenomic-pipelines.bib
+  - assets/references/authentication.bib
+  - assets/references/chapter-template.bib
+  - assets/references/chapter-writing-guidelines.bib
+  - assets/references/contamination.bib
+  - assets/references/denovo-assembly.bib
+  - assets/references/genome-mapping.bib
+  - assets/references/git-github.bib
+  - assets/references/index.bib
+  - assets/references/introduction-to-ancient-dna.bib
+  - assets/references/introduction-to-edna.bib
+  - assets/references/introduction-to-ngs-sequencing.bib
+  - assets/references/phylogenomics.bib
+  - assets/references/r-tidyverse.bib
+  - assets/references/taxonomic-profiling.bib
+
 book:
   title: "Introduction to Ancient Metagenomics"
   author: "James A. Fellows Yates and Christina Warinner"
@@ -67,4 +85,5 @@ format:
       - assets/css/custom.scss
     cover-image: assets/images/cover.png
   # pdf:
-  #   documentclass: scrreprt
+  #   documentclass: book
+  #   biblio-title: "References"
diff --git a/assets/images/chapters/bare-bones-bash/cc-sa-4.0-88x31.png b/assets/images/chapters/bare-bones-bash/cc-sa-4.0-88x31.png
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-3dhelix.png b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-3dhelix.png
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-ancientdnainbone.png b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-ancientdnainbone.png
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-bridgeamplification.png b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-bridgeamplification.png
diff --git a/...tro-to-ngs/fig-intro-ngs-chromatogram.jpg → ...to-ngs/fig-intro-ngs-fig-chromatogram.jpg b/...tro-to-ngs/fig-intro-ngs-chromatogram.jpg → ...to-ngs/fig-intro-ngs-fig-chromatogram.jpg
diff --git a/...ages/chapters/intro-to-ngs/fig-intro-ngs-fig-contamination-blog-screenshots.png b/...ages/chapters/intro-to-ngs/fig-intro-ngs-fig-contamination-blog-screenshots.png
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-demultiplexing.png b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-demultiplexing.png
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-fastqc.png b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-fastqc.png
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-flowcell.png b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-flowcell.png
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-flowcellschematic.png b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-flowcellschematic.png
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-grassy-lawn.jpg b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-grassy-lawn.jpg
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-indexhopping.jpg b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-indexhopping.jpg
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-library-construct.png b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-library-construct.png
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-moderndnaextraction.jpg b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-moderndnaextraction.jpg
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-pairedendsequencing.png b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-pairedendsequencing.png
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-read-stacking.png b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-read-stacking.png
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-sbsimagecapture.png b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-sbsimagecapture.png
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-sequencing-read.png b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-sequencing-read.png
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-sequencingbysynthesis.png b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-sequencingbysynthesis.png
diff --git a/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-twocolourchemistry.png b/assets/images/chapters/intro-to-ngs/fig-intro-ngs-fig-twocolourchemistry.png
diff --git a/assets/images/chapters/python-pandas/SPAAM-Logo-Full-Colour_ShortName.svg b/assets/images/chapters/python-pandas/SPAAM-Logo-Full-Colour_ShortName.svg
diff --git a/assets/images/chapters/python-pandas/bar_plot.png b/assets/images/chapters/python-pandas/bar_plot.png
diff --git a/assets/images/chapters/python-pandas/boxplot.png b/assets/images/chapters/python-pandas/boxplot.png
diff --git a/assets/images/chapters/python-pandas/facet_scatter.png b/assets/images/chapters/python-pandas/facet_scatter.png
diff --git a/assets/images/chapters/python-pandas/fixed_histogram.png b/assets/images/chapters/python-pandas/fixed_histogram.png
diff --git a/assets/images/chapters/python-pandas/histogram.png b/assets/images/chapters/python-pandas/histogram.png
diff --git a/assets/images/chapters/python-pandas/scatter_polt_01.png b/assets/images/chapters/python-pandas/scatter_polt_01.png
diff --git a/assets/images/chapters/python-pandas/scatter_polt_02.png b/assets/images/chapters/python-pandas/scatter_polt_02.png