Merge pull request #38 from metagenlab/citation

Add paper citation

CITATION.cff

@@ -38,4 +38,17 @@ url: "https://metagenlab.github.io/MeSS/"
 abstract: >-
   Snakemake pipeline for simulating shotgun metagenomic samples
 license: MIT
-version: 0.10.0
+preferred-citation:
+  type: article
+  authors:
+    - given-names: Farid
+      family-names: Chaabane
+    - given-names: Trestan
+      family-names: Pillonel
+    - given-names: Claire
+      family-names: Bertelli
+  doi: "10.1093/bioinformatics/btae760"
+  journal: "Bioinformatics"
+  title: "MeSS and assembly_finder: A toolkit for in silico metagenomic sample generation"
+  year: 2024
+  url: "https://doi.org/10.1093/bioinformatics/btae760"

README.md

@@ -11,6 +11,7 @@
 [![docker](https://github.com/metagenlab/MeSS/actions/workflows/docker-publish.yml/badge.svg)](https://github.com/metagenlab/MeSS/actions/workflows/docker-publish.yml)
 
 [![DOI](https://zenodo.org/badge/195021481.svg)](https://zenodo.org/badge/latestdoi/195021481)
+[![paper](https://img.shields.io/badge/paper-Bioinformatics-%23167da4)](https://doi.org/10.1093/bioinformatics/btae760)
 
 The Metagenomic Sequence Simulator (MeSS) is a [Snakemake](https://github.com/snakemake/snakemake) pipeline, implemented using [Snaketool](https://github.com/beardymcjohnface/Snaketool), for simulating illumina, Oxford Nanopore (ONT) and Pacific Bioscience (PacBio) shotgun metagenomic samples.
 
@@ -251,3 +252,9 @@ mess run -i phage.tsv --rotate 3 -o mess_out/circular
 All command-line options at described [here](https://metagenlab.github.io/MeSS/commands/)
 
 ![`mess -h`](docs/images/mess-help.svg)
+
+## Citation
+
+Please consider citing `MeSS` if you use it in your work.
+
+> Farid Chaabane, Trestan Pillonel, Claire Bertelli, MeSS and assembly_finder: A toolkit for in silico metagenomic sample generation, Bioinformatics, 2024;, btae760, https://doi.org/10.1093/bioinformatics/btae760

mess/mess.CITATION

@@ -1,5 +1,5 @@
 Please cite MeSS and assembly_finder in your paper using this article:
-
+https://doi.org/10.1093/bioinformatics/btae760
 
 Please consider also citing these dependencies:
 ART: