update paper information (#60)

README.md

@@ -1,15 +1,15 @@
 <img src="assets/lOGO_3.png" width="300px">
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3997375.svg)](https://doi.org/10.5281/zenodo.3445485)
-[![Releases](https://img.shields.io/github/v/release/fmalmeida/mpgap)](https://github.com/fmalmeida/mpgap/releases)
+[![F1000 Paper](https://img.shields.io/badge/Citation%20F1000-10.12688/f1000research.139488.1-orange)](https://doi.org/10.12688/f1000research.139488.1)
+[![Github Releases](https://img.shields.io/github/v/release/fmalmeida/mpgap)](https://github.com/fmalmeida/mpgap/releases)
 [![Documentation](https://img.shields.io/badge/Documentation-readthedocs-brightgreen)](https://mpgap.readthedocs.io/en/latest/?badge=latest)
-[![Dockerhub](https://img.shields.io/badge/Docker-fmalmeida/mpgap-informational)](https://hub.docker.com/r/fmalmeida/mpgap)
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.04.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-[![Follow on Twitter](http://img.shields.io/badge/twitter-%40fmarquesalmeida-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/fmarquesalmeida)
 [![License](https://img.shields.io/badge/License-GPL%203-black)](https://github.com/fmalmeida/mpgap/blob/master/LICENSE)
+[![Zenodo Archive](https://zenodo.org/badge/DOI/10.5281/zenodo.3997375.svg)](https://doi.org/10.5281/zenodo.3445485)
+[![Follow on Twitter](http://img.shields.io/badge/twitter-%40fmarquesalmeida-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/fmarquesalmeida)
 
 <p align="center">
 

docs/index.rst

@@ -45,6 +45,15 @@ It wraps up the following tools:
    manual
    config
 
+Citation
+--------
+
+In order to cite this pipeline, please refer to:
+
+> Almeida FMd, Campos TAd and Pappas Jr GJ. Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation. [version 1; peer review: awaiting peer review]. F1000Research 2023, 12:1205 (https://doi.org/10.12688/f1000research.139488.1)
+
+Additionally, archived versions of the pipeline are also found in `Zenodo <https://doi.org/10.5281/zenodo.3445485>`_.
+
 Support Contact
 ---------------
 Whenever a doubt arise feel free to contact me at almeidafmarques@gmail.com

lib/WorkflowMain.groovy

@@ -10,7 +10,7 @@ class WorkflowMain {
     public static String citation(workflow) {
         return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
             "* The pipeline\n" +
-            "  https://doi.org/10.5281/zenodo.3445485\n\n" +
+            "  https://doi.org/10.12688/f1000research.139488.1\n\n" +
             "* The nf-core framework\n" +
             "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
             "* Software dependencies\n" +