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Sync dev to master #58

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merged 3 commits into from
Feb 21, 2024
Merged

Sync dev to master #58

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7605a53
Merge pull request #54 from nf-core/dev
kbestak Feb 12, 2024
6cadb9c
Replaced placeholder Zenodo DOIs
kbestak Feb 21, 2024
6909f24
Merge pull request #1 from kbestak/zenodo_update
maxulysse Feb 21, 2024
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5 changes: 2 additions & 3 deletions README.md
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@@ -1,7 +1,7 @@
# ![nf-core/molkart](docs/images/nf-core-molkart_logo_light.png#gh-light-mode-only) ![nf-core/molkart](docs/images/nf-core-molkart_logo_dark.png#gh-dark-mode-only)

[![GitHub Actions CI Status](https://github.com/nf-core/molkart/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/molkart/actions?query=workflow%3A%22nf-core+CI%22)
[![GitHub Actions Linting Status](https://github.com/nf-core/molkart/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/molkart/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/molkart/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
[![GitHub Actions Linting Status](https://github.com/nf-core/molkart/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/molkart/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/molkart/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10650749-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10650749)

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
Expand Down Expand Up @@ -91,8 +91,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#

## Citations

<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
<!-- If you use nf-core/molkart for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
If you use nf-core/molkart for your analysis, please cite it using the following doi: [10.5281/zenodo.10650749](https://doi.org/10.5281/zenodo.10650749)

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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5 changes: 2 additions & 3 deletions lib/WorkflowMain.groovy
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Expand Up @@ -11,9 +11,8 @@ class WorkflowMain {
//
public static String citation(workflow) {
return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
// TODO nf-core: Add Zenodo DOI for pipeline after first release
//"* The pipeline\n" +
//" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
"* The pipeline\n" +
" https://doi.org/10.5281/zenodo.10650749\n\n" +
"* The nf-core framework\n" +
" https://doi.org/10.1038/s41587-020-0439-x\n\n" +
"* Software dependencies\n" +
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