Merge pull request #27 from metagenlab/citation

Add paper citation

CITATION.cff

@@ -31,12 +31,25 @@ authors:
     orcid: 'https://orcid.org/0000-0003-0550-8981'
 identifiers:
   - type: doi
-    value: 10.5281/zenodo.13353494
-    description: zenodo software
+    value: 10.5281/zenodo.13985668
+    description: zenodo
 repository-code: 'https://github.com/metagenlab/assembly_finder'
 url: 'https://metagenlab.github.io/assembly_finder/'
 abstract: >-
   Snakemake-powered cli to download genomes using NCBI
   datasets 
 license: MIT
-version: 0.8.0
+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

@@ -9,6 +9,7 @@
 [![downloads](https://img.shields.io/conda/dn/bioconda/assembly_finder)](https://anaconda.org/bioconda/assembly_finder)
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13353494.svg)](https://zenodo.org/doi/10.5281/zenodo.13353494)
+[![paper](https://img.shields.io/badge/paper-Bioinformatics-%23167da4)](https://doi.org/10.1093/bioinformatics/btae760)
 
 `assembly_finder` is a [Snakemake](https://github.com/snakemake/snakemake)-powered cli, written in [Snaketool](https://github.com/beardymcjohnface/Snaketool), to download genomes with [NCBI datasets](https://github.com/ncbi/datasets).  
 
@@ -72,3 +73,9 @@ You can find more information on assembly_finder's inputs, outputs and example c
 ## :scroll: Help
 
 ![`assembly_finder -h`](docs/images/af-help.svg)
+
+## Citation
+
+Please consider citing `assembly_finder` 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

assembly_finder/assembly_finder.CITATION

@@ -1,9 +1,18 @@
-Please cite Assembly finder in your paper using this article:
+Please cite assembly_finder using this article:
+https://doi.org/10.1093/bioinformatics/btae760
 
 
 Please consider also citing these dependencies:
+
 Snaketool:
 https://doi.org/10.1371/journal.pcbi.1010705
 
 Snakemake:
 https://doi.org/10.12688/f1000research.29032.1
+
+NCBI datasets:
+https://doi.org/10.1038/s41597-024-03571-y
+
+Taxonkit:
+https://doi.org/10.1016/j.jgg.2021.03.006
+