From 61411b6f3feb6314cf4d1a5192026d457a9c31b4 Mon Sep 17 00:00:00 2001 From: d4straub Date: Fri, 29 Oct 2021 13:51:26 +0200 Subject: [PATCH 1/3] add preprint info --- CHANGELOG.md | 5 +++-- README.md | 11 ++++++++++- lib/WorkflowMain.groovy | 2 ++ 3 files changed, 15 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5add0c2b..18e61ab7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,8 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` --[#240](https://github.com/nf-core/mag/pull/240) - Add prodigal to predict protein-coding genes for assemblies --[#241](https://github.com/nf-core/mag/pull/241) - Add parameter `--skip_prodigal` +-[#240](https://github.com/nf-core/mag/pull/240) - Add prodigal to predict protein-coding genes for assemblies. +-[#241](https://github.com/nf-core/mag/pull/241) - Add parameter `--skip_prodigal`. +-[#243](https://github.com/nf-core/mag/pull/241) - Add pipeline preprint information. ### `Changed` diff --git a/README.md b/README.md index 63c74393..bffdc49e 100644 --- a/README.md +++ b/README.md @@ -4,6 +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) [![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/) @@ -104,7 +105,15 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations -If you use nf-core/mag for your analysis, please cite it using the following doi: [10.5281/zenodo.3589527](https://doi.org/10.5281/zenodo.3589527) +If you use nf-core/mag for your analysis, please cite the preprint as follows: + +> **nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning** +> +> 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). + +additionally you can cite the pipeline directly with the following doi: [10.5281/zenodo.3589527](https://doi.org/10.5281/zenodo.3589527) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 27c54339..553994ca 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -9,6 +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\n" + " https://doi.org/10.5281/zenodo.3589527\n\n" + "* The nf-core framework\n" + From 73827c392c700fd937b6f3ea7adcb8e2f8643a03 Mon Sep 17 00:00:00 2001 From: d4straub Date: Fri, 29 Oct 2021 14:08:52 +0200 Subject: [PATCH 2/3] fix PR no --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 18e61ab7..275edaf0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 -[#240](https://github.com/nf-core/mag/pull/240) - Add prodigal to predict protein-coding genes for assemblies. -[#241](https://github.com/nf-core/mag/pull/241) - Add parameter `--skip_prodigal`. --[#243](https://github.com/nf-core/mag/pull/241) - Add pipeline preprint information. +-[#244](https://github.com/nf-core/mag/pull/244) - Add pipeline preprint information. ### `Changed` From 17a07705f0d72e8841c1a1837f49ae0fde61a809 Mon Sep 17 00:00:00 2001 From: Daniel Straub <42973691+d4straub@users.noreply.github.com> Date: Fri, 29 Oct 2021 14:33:15 +0200 Subject: [PATCH 3/3] Update CHANGELOG.md Co-authored-by: AntoniaSchuster <56543138+AntoniaSchuster@users.noreply.github.com> --- CHANGELOG.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 275edaf0..089da293 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,9 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` --[#240](https://github.com/nf-core/mag/pull/240) - Add prodigal to predict protein-coding genes for assemblies. --[#241](https://github.com/nf-core/mag/pull/241) - Add parameter `--skip_prodigal`. --[#244](https://github.com/nf-core/mag/pull/244) - Add pipeline preprint information. +- [#240](https://github.com/nf-core/mag/pull/240) - Add prodigal to predict protein-coding genes for assemblies. +- [#241](https://github.com/nf-core/mag/pull/241) - Add parameter `--skip_prodigal`. +- [#244](https://github.com/nf-core/mag/pull/244) - Add pipeline preprint information. ### `Changed`