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add preprint info #244

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Oct 29, 2021
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add preprint info #244

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61411b6
add preprint info
d4straub Oct 29, 2021
73827c3
fix PR no
d4straub Oct 29, 2021
17a0770
Update CHANGELOG.md
d4straub Oct 29, 2021
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5 changes: 3 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -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`.
- [#244](https://github.com/nf-core/mag/pull/244) - Add pipeline preprint information.

### `Changed`

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11 changes: 10 additions & 1 deletion README.md
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Expand Up @@ -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/)
Expand Down Expand Up @@ -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.

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2 changes: 2 additions & 0 deletions lib/WorkflowMain.groovy
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Expand Up @@ -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" +
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