add citation

.gitignore

@@ -19,4 +19,5 @@ _site
 .Renviron
 
 # Jupyter cache
-.jupyter_cache
+.jupyter_cache
+/.luarc.json

CITATION.cff

@@ -0,0 +1,30 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: Working with Bacterial Genomes
+message: >-
+  You may cite these materials using the metadata in this
+  file. Please cite our materials if you publish materials
+  derived from these, run a workshop using them, or use
+  the   information in your own work.
+type: dataset
+authors:
+  - given-names: Andries
+    family-names: van Tonder
+    orcid: 'https://orcid.org/0000-0002-4380-5250'
+    affiliation: >-
+      Department of Veterinary Medicine, University of
+      Cambridge
+  - given-names: Hugo
+    family-names: Tavares
+    affiliation: Cambridge Centre for Research Informatics Training
+    orcid: 'https://orcid.org/0000-0001-9373-2726'
+  - given-names: Bajuna
+    family-names: Salehe
+    affiliation: Cambridge Centre for Research Informatics Training
+repository-code: 'https://github.com/cambiotraining/bacterial-genomics'
+url: 'https://cambiotraining.github.io/bacterial-genomics/'
+license: CC-BY-4.0
+commit: TODO
+date-released: '2024-07-22'

index.md

@@ -48,55 +48,24 @@ The course is aimed at biologists interested in microbiology, prokaryotic genomi
 - A working knowledge of running analysis on High Performance Computing (HPC) clusters (course registration page).
 
 
-## Authors
-<!-- 
-The listing below shows an example of how you can give more details about yourself.
-These examples include icons with links to GitHub and Orcid. 
--->
-
-About the authors:
-
-- **Andries van Tonder**
-  <a href="https://orcid.org/0000-0002-4380-5250" target="_blank"><i class="fa-brands fa-orcid" style="color:#a6ce39"></i></a> 
-  <a href="https://github.com/avantonder" target="_blank"><i class="fa-brands fa-github" style="color:#4078c0"></i></a>  
-  _Affiliation_: Department of Veterinary Medicine, University of Cambridge  
-  _Roles_: writing - original draft; conceptualisation; coding
-- **Hugo Tavares**
-  <a href="https://orcid.org/0000-0001-9373-2726" target="_blank"><i class="fa-brands fa-orcid" style="color:#a6ce39"></i></a> 
-  <a href="https://github.com/tavareshugo" target="_blank"><i class="fa-brands fa-github" style="color:#4078c0"></i></a>  
-  _Affiliation_: Bioinformatics Training Facility, University of Cambridge  
-  _Roles_: writing - review & editing
-- **Bajuna Salehe**
-  <a href="https://github.com/bsalehe" target="_blank"><i class="fa-brands fa-github" style="color:#4078c0"></i></a>  
-  _Affiliation_: Bioinformatics Training Facility, University of Cambridge  
-  _Roles_: writing - original content; conceptualisation; coding; data curation
-
-
-## Citation
+## Citation & Authors
 
-<!-- We can do this at the end -->
+:::{.callout-important}
+These materials are a fork of the [Carpentries Shell Lesson](https://swcarpentry.github.io/shell-novice/).  
+As such, please make sure to cite both works if you use these materials (see [Acknowledgements]).
+:::
 
 Please cite these materials if:
 
 - You adapted or used any of them in your own teaching.
-- These materials were useful for your research work. For example, you can cite us in the methods section of your paper: "We carried our analyses based on the recommendations in _TODO_.".
-
-You can cite these materials as:
-
-> TODO
+- These materials were useful for your research work. For example, you can cite us in the methods section of your paper: "We carried our analyses based on the recommendations in _YourReferenceHere_".
 
-Or in BibTeX format:
+<!-- 
+This is generated automatically from the CITATION.cff file. 
+If you think you should be added as an author, please get in touch with us.
+-->
 
-```
-@Misc{,
-  author = {},
-  title = {},
-  month = {},
-  year = {},
-  url = {},
-  doi = {}
-}
-```
+{{< citation CITATION.cff >}}
 
 
 ## Acknowledgements