Update README.md

README.md

@@ -17,7 +17,12 @@ ARETE produces a range of useful outputs, including those generated by each tool
 ARETE has been applied to datasets ranging from fewer than ten to over 10,000 genomes from a multitude of species and genera including _Enterococcus faecium_, _Escherichia coli_, _Listeria_, and _Salmonella_. Although ARETE was primarily developed with pathogens in mind, inference of pan-genomes, mobilomes, and phylogenomic histories can be performed for any set of microbial genomes, with the proviso that reference databases are much more complete for some groups than others! The tools in ARETE work best at the species and genus level of relatedness.
 
 # Table of Contents
-1.[About the pipeline](#about)
+1. [About the pipeline](#about)
+2. [Quick start](#quickstart)
+3. [Documentation](#documentation)
+4. [Credits](#credits)
+5. [Contributing to ARETE](#contributing)
+6. [Citations](#citations)
 
 ## About the pipeline <a name="about"></a>
 
@@ -71,7 +76,7 @@ Check recombination events within each PopPUNK cluster.
 
 See our [roadmap](ROADMAP.md) for future development targets.
 
-## Quick Start
+## Quick Start <a name="quickstart"></a>
 
 1.  Install [`nextflow`](https://nf-co.re/usage/installation)
 
@@ -123,21 +128,21 @@ nextflow run beiko-lab/ARETE \
   --bakta_db $PWD/baktadb/db-light
 ```
 
-## Documentation
+## Documentation <a name="documentation"></a>
 
 The ARETE pipeline comes with documentation about the pipeline: [usage](https://beiko-lab.github.io/arete/usage/) and [output](https://beiko-lab.github.io/arete/output/).
 
-## Credits
+## Credits <a name="credits"></a>
 
 ARETE was originally written and developed by [Finlay Maguire](https://github.com/fmaguire) and [Alex Manuele](https://github.com/alexmanuele), and is currently developed by [João Cavalcante](https://github.com/jvfe).
 
-## Contributions and Support
+## Contributing to ARETE <a name="contributing"></a>
 
 <!--If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).-->
 
 Thank you for your interest in contributing to ARETE. We are currently in the process of formalizing contribution guidelines. In the meantime, please feel free to open an issue describing your suggested changes.
 
-## Citations
+## Citations <a name="citations"></a>
 
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->