Merge branch 'master' into functional_tests

README.md

 # **PanACoTA**
  [![License (AGPL version 3)](https://img.shields.io/badge/license-GNU%20AGPL%20version%203-blue.svg)](COPYING)
 [![https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/4724)
+[![DOI:10.1101/2020.09.11.293472](https://zenodo.org/badge/DOI/10.1101/2020.09.11.293472.svg)](https://doi.org/10.1101/2020.09.11.293472)
 
+[![GitHub release](https://img.shields.io/github/release/gem-pasteur/PanACoTA.svg)](https://github.com/gem-pasteur/PanACoTA/releases)
 [![pipeline status](https://gitlab.pasteur.fr/aperrin/pipeline_annotation/badges/master/pipeline.svg)](https://gitlab.pasteur.fr/aperrin/pipeline_annotation/-/pipelines)
 <!---
 [![coverage report](https://gitlab.pasteur.fr/aperrin/pipeline_annotation/badges/master/coverage.svg)](http://aperrin.pages.pasteur.fr/pipeline_annotation/htmlcov)
@@ -27,7 +29,8 @@ This README file provides some essential information to install/use PanACoTA. Bu
 
 If you use PanACoTA, please cite:
 
-PERRIN, A., & ROCHA, E. (2020). PanACoTA: A modular tool for massive microbial comparative genomics. BioRxiv. https://doi.org/10.1101/2020.09.11.293472
+Amandine PERRIN, Eduardo P.C. ROCHA (2020).  PanACoTA: A modular tool for massive microbial comparative genomics. BioRxiv. 
+[![DOI:10.1101/2020.09.11.293472](https://zenodo.org/badge/DOI/10.1101/2020.09.11.293472.svg)](https://doi.org/10.1101/2020.09.11.293472)
 
 
 # Installation
@@ -142,6 +145,8 @@ You can find more information in [PanACoTA documentation](http://aperrin.pages.p
 
 ## On cluster
 
+[![https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/4724)
+
 We provide a singularity image, to help running PanACoTA on a cluster.
 
 First, download the singularity image:

doc/source/index.rst

@@ -5,7 +5,7 @@ Welcome to PanACoTA's documentation!
 
 If you use PanACoTA, please cite:
 
-PERRIN, A., & ROCHA, E. (2020). PanACoTA: A modular tool for massive microbial comparative genomics. BioRxiv. https://doi.org/10.1101/2020.09.11.293472
+Amandine PERRIN, Eduardo P.C. ROCHA (2020). PanACoTA: A modular tool for massive microbial comparative genomics. BioRxiv. https://doi.org/10.1101/2020.09.11.293472