From 222689f6053381872c1d4103a8ae24eff90ee076 Mon Sep 17 00:00:00 2001 From: d4straub Date: Wed, 23 Mar 2022 14:53:34 +0100 Subject: [PATCH 1/2] add publication --- CHANGELOG.md | 1 + README.md | 4 ++-- lib/WorkflowMain.groovy | 4 ++-- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 96f94b7e..af021b0b 100644 --- a/CHANGELOG.md +++ b/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` diff --git a/README.md b/README.md index b86fb617..3ecec220 100644 --- a/README.md +++ b/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 Publucation](https://img.shields.io/badge/Cite%20Us!-Cite%20Preprint-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) diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index d9883bce..e85e510c 100755 --- a/lib/WorkflowMain.groovy +++ b/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" + From 80d9026e1bd521513956b528c1cfe8f48f32b66d Mon Sep 17 00:00:00 2001 From: Daniel Straub <42973691+d4straub@users.noreply.github.com> Date: Wed, 23 Mar 2022 15:02:27 +0100 Subject: [PATCH 2/2] Update README.md Co-authored-by: James A. Fellows Yates --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3ecec220..1c705613 100644 --- a/README.md +++ b/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 Publucation](https://img.shields.io/badge/Cite%20Us!-Cite%20Preprint-orange)](https://doi.org/10.1093/nargab/lqac007) +[![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/)