Merge pull request #131 from SPAAM-community/update-all-zenodo-for-2025

jfy133 · web-flow · commit e232ab768ed7 · 2025-09-19T08:52:49.000+01:00
Update all chapter dataset links to new Zenodo uploads for 2025 updated datasets
diff --git a/accessing-ancient-metagenomic-data.qmd b/accessing-ancient-metagenomic-data.qmd
@@ -10,7 +10,7 @@ bibliography: assets/references/accessing-ancient-metagenomic-data.bib
 ::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
 For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.
 
-Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759163](https://doi.org/10.5281/zenodo.13759163), and unpack
+Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17155430](https://doi.org/10.5281/zenodo.17155430), and unpack
 
 ```bash
 tar xvf accessing-ancient-metagenomic-data.tar.gz 
diff --git a/ancient-metagenomic-pipelines.qmd b/ancient-metagenomic-pipelines.qmd
@@ -8,7 +8,7 @@ bibliography: assets/references/ancient-metagenomic-pipelines.bib
 For this chapter's exercises, if not already performed, we will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.
 
 Do this, use `wget` or right click and save to download this Zenodo archive: 
-[10.5281/zenodo.13759201](https://doi.org/10.5281/zenodo.13759201), and unpack.
+[10.5281/zenodo.17155341](https://doi.org/10.5281/zenodo.17155341), and unpack.
 
 ```bash
 tar xvf ancient-metagenomic-pipelines.tar.gz 
diff --git a/authentication.qmd b/authentication.qmd
@@ -7,7 +7,7 @@ bibliography: assets/references/authentication.bib
 ::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
 For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.
 
-Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759228](https://doi.org/10.5281/zenodo.13759228), and unpack
+Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17152964](https://doi.org/10.5281/zenodo.17152964), and unpack
 
 ```bash
 tar xvf authentication.tar.gz 
diff --git a/bare-bones-bash.qmd b/bare-bones-bash.qmd
@@ -6,7 +6,7 @@ author: Thiseas C. Lamnidis, Aida Andrades Valtueña
 ::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
 For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.
 
-Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759270](https://doi.org/10.5281/zenodo.13759270), and unpack.
+Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17155440](https://doi.org/10.5281/zenodo.17155440), and unpack.
 
 ```bash
 tar xvf bare-bones-bash.tar.gz 
diff --git a/contamination.qmd b/contamination.qmd
@@ -7,7 +7,7 @@ bibliography: assets/references/contamination.bib
 ::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
 For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.
 
-Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759285](https://doi.org/10.5281/zenodo.13759285), and unpack
+Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17155413](https://doi.org/10.5281/zenodo.17155413), and unpack
 
 ```bash
 tar xvf contamination.tar.gz
diff --git a/denovo-assembly.qmd b/denovo-assembly.qmd
@@ -13,7 +13,7 @@ library(pander)
 ::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
 For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.
 
-Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759302](https://doi.org/10.5281/zenodo.13759302), and unpack
+Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17142958](https://doi.org/10.5281/zenodo.17142958), and unpack
 
 ```bash
 tar xvf denovo-assembly.tar.gz 
diff --git a/genome-mapping.qmd b/genome-mapping.qmd
@@ -7,7 +7,7 @@ bibliography: assets/references/genome-mapping.bib
 :::{.callout-note collapse="true" title="Self guided: chapter environment setup"}
 For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.
 
-Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759321](https://doi.org/10.5281/zenodo.13759321), and unpack.
+Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17154630](https://doi.org/10.5281/zenodo.17154630), and unpack.
 
 ```bash
 tar xvf genome-mapping.tar.gz 
diff --git a/git-github.qmd b/git-github.qmd
@@ -7,7 +7,7 @@ bibliography: assets/references/git-github.bib
 ::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
 For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.
 
-Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759333](https://doi.org/10.5281/zenodo.13759333), and unpack.
+Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17155418](https://doi.org/10.5281/zenodo.17155418), and unpack.
 
 ```bash
 tar xvf git-github.tar.gz 
diff --git a/phylogenomics.qmd b/phylogenomics.qmd
@@ -7,7 +7,7 @@ bibliography: assets/references/phylogenomics.bib
 ::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
 For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.
 
-Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13759782](https://doi.org/10.5281/zenodo.13759782), and unpack.
+Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17155402](https://doi.org/10.5281/zenodo.17155402), and unpack.
 
 ```bash
 tar xvf phylogenomics.tar.gz 
diff --git a/python-pandas.qmd b/python-pandas.qmd
@@ -10,7 +10,7 @@ This session is typically ran held in parallel to the Introduction to R and Tidy
 ::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
 For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.
 
-Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.11394586](https://doi.org/10.5281/zenodo.11394586), and unpack
+Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17155406](https://doi.org/10.5281/zenodo.17155406), and unpack
 
 ```bash
 tar xvf python-pandas.tar.gz 
diff --git a/r-tidyverse.qmd b/r-tidyverse.qmd
@@ -19,7 +19,7 @@ We recommend this session if you have no experience with neither R nor Python.
 ::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
 For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.
 
-To do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13758879](https://doi.org/10.5281/zenodo.13758879), and unpack
+To do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17155415](https://doi.org/10.5281/zenodo.17155415), and unpack
 
 ```bash
 tar xvf r-tidyverse.tar.gz 
diff --git a/taxonomic-profiling.qmd b/taxonomic-profiling.qmd
@@ -7,7 +7,7 @@ bibliography: assets/references/taxonomic-profiling.bib
 ::: {.callout-note collapse="true" title="Self guided: chapter environment setup"}
 For this chapter's exercises, if not already performed, you will need to download the chapter's dataset, decompress the archive, and create and activate the conda environment.
 
-Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.13760277](https://doi.org/10.5281/zenodo.13760277), and unpack
+Do this, use `wget` or right click and save to download this Zenodo archive: [10.5281/zenodo.17155271](https://doi.org/10.5281/zenodo.17155271), and unpack
 
 ```bash
 tar xvf taxonomic-profiling.tar.gz 
