Merge branch 'main' of github.com:SPAAM-community/intro-to-ancient-metagenomics-book

Author: jfy133

.gitpod.yml

@@ -15,6 +15,9 @@ authors:
   - family-names: Borry
     given-names: Maxime
     orcid: https://orcid.org/0000-0001-9140-7559
+  - family-names: Denise
+    given-names: Rémi
+    orcid: https://orcid.org/0000-0003-2277-689X
   - family-names: Guellil
     given-names: Meriam
     orcid: https://orcid.org/0000-0002-7235-4604
@@ -64,11 +67,11 @@ authors:
     orcid: https://orcid.org/0009-0000-2068-3505
 
 title: "Introduction to Ancient Metagenomics"
-version: 2024
+version: 2025.1
 doi: 10.5281/zenodo.8027280
-date-released: 2024-09-17
+date-released: 2025-11-25
 license: CC-BY-4.0
-license_url: https://github.com/SPAAM-community/intro-to-ancient-metagenomics-book/blob/2024.1/LICENSE
+license_url: https://github.com/SPAAM-community/intro-to-ancient-metagenomics-book/blob/2025.1/LICENSE
 keywords:
   - "ancient metagenomics"
   - metagenomics

CITATION.cff

@@ -10,36 +10,7 @@ This is the source material for the [Introduction to Ancient Metagenomics text b
 
 This text book has been developed as a [Quarto](https://quarto.org/) Book, allowing for both website and PDF formats.
 
-It is highly recommend to use the [Gitpod environment](#gitpod) to develop new material for the textbook, as it provides a fully set up writing environment.
-
-If running [locally](#locally), I highly recommend installing [VS Code](https://code.visualstudio.com/) (or your [preferred text editor/IDE](https://quarto.org/docs/get-started/)) and the corresponding [Quarto extension](https://quarto.org/docs/getting-started/installation.html#vs-code-extension) for development. This allows rendering prior to pushing to GitHub, and debugging of any issues of the website view. Make sure you also install all the dependincy requirements as described in the `.gitpod.Dockerfile`
-
-### GitPod
-
-1. Fork this repository
-2. Open on [https://gitpod.io](https://gitpod.io) [^1]
-   - This may take a little bit of time to pull the docker container
-   - Once loaded, wait a minute or so until the preview of the textbook is loaded (you will see lots of text being printed in the console)
-   - To load the preview, press the 'open preview' button in the bottom right
-     ![image](https://github.com/SPAAM-community/intro-to-ancient-metagenomics-book/assets/17950287/cc47d264-eb4e-4fff-94c8-a8da21e9494b)
-   - If you miss the message above, press 'Ports' in the bottom right toolbar, and click the running URL to open in a new tab
-3. Make a new branch e.g. `git switch -c new-chapter`
-4. If adding a new chapter, make a new `.qmd` file in the root directory, else edit the existing `.qmd` file of your choice
-5. Images for the chapter should go into `assets/images/chapters/`
-   - Do not place in `docs/assets/images/chapters/`!
-6. References in BibTex for the chapter should go a `references.bib` file into `assets/references/<chapter_name>.bib`
-7. Conda environment files go in `docs/assets/envs/<chapter_name>.bib`
-8. If adding a new chapter, add the `.qmd` file to the `_quarto.yml` config file in the `chapters:` scope
-9. Refresh the preview tab to check your chapter renders correctly
-10. Commit, push to GitHub, and open a PR against the `main` branch [^2]
-
-> ![WARNING]
-> Only push `.qmd`, images, `.bib` files etc! Do not push `html` `json` files etc., from the rendering!
-
-General tips:
-
-- Use the native markdown syntax for images (`![](assets/images/chapters/<your_image>.png)`)
-- For note blocks see the [Quarto docs](https://quarto.org/docs/authoring/callouts.html#callout-types)
+If running [locally](#locally), I highly recommend installing [VS Code](https://code.visualstudio.com/) (or your [preferred text editor/IDE](https://quarto.org/docs/get-started/)) and the corresponding [Quarto extension](https://quarto.org/docs/getting-started/installation.html#vs-code-extension) for development. This allows rendering prior to pushing to GitHub, and debugging of any issues of the website view. Make sure you also install all the dependincy requirements as described in the `Dockerfile`
 
 ### Locally
 
@@ -75,7 +46,7 @@ General tips:
 - Check for any major TODOs in the book
 - Make sure authors updated
   - On authors.qmd
-  - In citations.gff
+  - In citations.cff
   - In citing-this-book.qmd (set DOI to root DOI)
 - Make sure cover images updated
   - Stating (Edition 202X)
@@ -86,7 +57,7 @@ General tips:
   - Make sure to bump year to title
   - Version system: YYYY.point release (2024.0, 2024.1)
   - Make sure to update authors if required
-- Update Zenodo DOI for each chapter
+- Update Zenodo DOI for in each chapter DOI
 - Make sure footnotes year fixed everywhere (\_quarto.yml)
 - Update release date in citations.cff
 
@@ -95,6 +66,3 @@ General tips:
 - In citing-this-book.qmd set DOI to release DOI
 
 ## Notes
-
-[^1]: I recommend installing the [gitpod chrome extension](https://chrome.google.com/webstore/detail/gitpod-always-ready-to-co/dodmmooeoklaejobgleioelladacbeki) which adds a nice shortcut button to the github repository next to the green 'code' button.
-[^2]: If you're using gitpod and have a 'don't have permissions' error when pushing you may need to do the following: (1) Go to: [https://gitpod.io/user/integrations](https://gitpod.io/user/integrations) (2) Press triple dots next to the GitHub Git Provider (3) Edit permissions so all permissions are ticked _except_ for `read:user`

.gitpod.Dockerfile Dockerfile.gitpod.Dockerfile renamed to Dockerfile

@@ -72,7 +72,7 @@ book:
 
   license: "CC-BY 4.0"
   cover-image: "assets/images/cover.png"
-  page-footer: "© 2024 SPAAM Community & Authors with ❤️. Available under [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/). Source material [here](https://github.com/SPAAM-community/intro-to-ancient-metagenomics-book)."
+  page-footer: "© 2025 SPAAM Community & Authors with ❤️. Available under [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/). Source material [here](https://github.com/SPAAM-community/intro-to-ancient-metagenomics-book)."
   site-url: https://spaam-community.github.org/intro-to-ancient-metagenomics-book
   favicon: favicon.png
   open-graph: true

README.md

@@ -112,7 +112,7 @@ In ancient DNA we need to use tools better suited for low coverage, and short re
 ### Running nf-core/eager
 
 For the practical portion of this chapter, we will utilise sequencing data from four aDNA libraries, which we should have already downloaded from NCBI.
-If not, please see the **Preparation** section above <!-- TODO Add download links & DOWNLOAD GFF FILE - SEE NOTE BELOW -->.
+If not, please see the **Preparation** section above.
 We will use nf-core/eager to perform a typical microbial _genomic_ analysis, i.e., reconstruction of an ancient genome to generate variant calls that can be used for generating phylogenomic trees and other evolutionary analysis, and gene feature coverage statistics to allow insight into the functional aspects of the genome.
 
 These four libraries come from from two ancient individuals, GLZ002 and KZL002.
@@ -127,11 +127,11 @@ Our aims in the following tutorial are to:
 1. Preprocess the FASTQ files by trimming adapters and merging paired-end reads
 2. Align reads to the _Y.
 pestis_ reference and compute the endogenous DNA percentage
-3. Filter the aligned reads to remove host DNA
-4. Remove duplicate reads for accurate coverage estimation and genotyping
-5. Generate statistics on gene features (e.g. virulence factors)
-6. Merge data by sample and perform genotyping on the combined dataset
-7. Review quality control data to evaluate the success of the previous steps
+1. Filter the aligned reads to remove host DNA
+2. Remove duplicate reads for accurate coverage estimation and genotyping
+3. Generate statistics on gene features (e.g. virulence factors)
+4. Merge data by sample and perform genotyping on the combined dataset
+5. Review quality control data to evaluate the success of the previous steps
 
 Let's get started!