Adding citations and new badges to docs

docs/index.md

@@ -3,9 +3,15 @@
   <h1 style="font-size: 250%">mir-seek 🔬</h1>
 
   <b><i>An awesome microRNA-sequencing pipeline</i></b><br>
+  <a href="https://doi.org/10.5281/zenodo.13834237">
+    <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.13834237.svg" alt="DOI">
+  </a>
+  <a href="https://github.com/OpenOmics/mir-seek/releases">
+    <img alt="GitHub release" src="https://img.shields.io/github/v/release/OpenOmics/mir-seek?color=blue&include_prereleases">
+  </a>
   <a href="https://hub.docker.com/repository/docker/skchronicles/mir-seek">
     <img alt="Docker Pulls" src="https://img.shields.io/docker/pulls/skchronicles/mir-seek">
-  </a> 
+  </a><br> 
   <a href="https://github.com/OpenOmics/mir-seek/actions/workflows/main.yaml">
     <img alt="tests" src="https://github.com/OpenOmics/mir-seek/workflows/tests/badge.svg">
   </a>
@@ -27,6 +33,7 @@
 
 
 ## Overview
+
 Welcome to mir-seek's documentation! This guide is the main source of documentation for users that are getting started with the [miR-sequencing pipeline](https://github.com/OpenOmics/mir-seek/). 
 
 The **`./mir-seek`** pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions: 
@@ -69,26 +76,39 @@ Before getting started, we highly recommend reading through the [usage](usage/ru
 
 For more information about issues or trouble-shooting a problem, please checkout our [FAQ](faq/questions.md) prior to [opening an issue on Github](https://github.com/OpenOmics/mir-seek/issues).
 
-## Contribute 
+## Contribute
 
 This site is a living document, created for and by members like you. mir-seek is maintained by the members of NCBR and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our [GitHub repository :octicons-heart-fill-24:{ .heart }](https://github.com/OpenOmics/mir-seek).
 
 ## Citation
 
+Please note that more citation formats and releases can be found on the [mir-seek zenodo page](https://doi.org/10.5281/zenodo.13834237).
+
 If you use this software, please cite it as below:  
 
 === "BibTex"
 
     ```
-    Citation coming soon!
+    @software{Kuhn_OpenOmics_mir-seek_2024,
+      author       = {Skyler, Kuhn and
+                      Gary, Zhang},
+      title        = {OpenOmics/mir-seek: v0.3.0},
+      month        = sep,
+      year         = 2024,
+      publisher    = {Zenodo},
+      version      = {v0.3.0},
+      doi          = {10.5281/zenodo.13834238},
+      url          = {https://doi.org/10.5281/zenodo.13834238}
+    }
     ```
 
 === "APA"
 
     ```
-    Citation coming soon!
+    Skyler, K., & Gary, Z. (2024). OpenOmics/mir-seek: v0.3.0 (v0.3.0). Zenodo. https://doi.org/10.5281/zenodo.13834238
     ```
 
 ## References
+
 <sup>**1.**  Kurtzer GM, Sochat V, Bauer MW (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5): e0177459.</sup>  
 <sup>**2.**  Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600.</sup>