Merge pull request #287 from d4straub/dev

add publication

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`
 
 - [#269](https://github.com/nf-core/mag/pull/269) - Update to nf-core 2.2 `TEMPLATE`
+- [#286](https://github.com/nf-core/mag/pull/286) - Cite our publication instead of the preprint
 
 ### `Fixed`
 

README.md

@@ -4,7 +4,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/mag/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/mag/actions?query=workflow%3A%22nf-core+linting%22)
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/mag/results)
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3589527-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3589527)
-[![Cite Preprint](https://img.shields.io/badge/Cite%20Us!-Cite%20Preprint-orange)](https://doi.org/10.1101/2021.08.29.458094)
+[![Cite Publication](https://img.shields.io/badge/Cite%20Us!-Cite%20Publication-orange)](https://doi.org/10.1093/nargab/lqac007)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.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/)
@@ -116,7 +116,7 @@ If you use nf-core/mag for your analysis, please cite the preprint as follows:
 >
 > Sabrina Krakau, Daniel Straub, Hadrien Gourlé, Gisela Gabernet, Sven Nahnsen.
 >
-> bioRxiv 2021.08.29.458094. doi: [10.1101/2021.08.29.458094](https://doi.org/10.1101/2021.08.29.458094).
+> NAR Genom Bioinform. 2022 Feb 2;4(1):lqac007. doi: [10.1093/nargab/lqac007](https://doi.org/10.1093/nargab/lqac007).
 
 additionally you can cite the pipeline directly with the following doi: [10.5281/zenodo.3589527](https://doi.org/10.5281/zenodo.3589527)
 

lib/WorkflowMain.groovy

@@ -9,8 +9,8 @@ class WorkflowMain {
     //
     public static String citation(workflow) {
         return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-            "* The preprint\n" +
-            "  https://doi.org/10.1101/2021.08.29.458094\n\n" +
+            "* The pipeline publication\n" +
+            "  https://doi.org/10.1093/nargab/lqac007\n\n" +
             "* The pipeline\n" +
             "  https://doi.org/10.5281/zenodo.3589527\n\n" +
             "* The nf-core framework\n" +