Merge pull request #59 from nf-core/dev (81ede336) · Commits · Chaos / Cutandrun

README.md

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		@@ -3,7 +3,7 @@
		[![GitHub Actions CI Status](https://github.com/nf-core/cutandrun/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/cutandrun/actions?query=workflow%3A%22nf-core+CI%22)
		[![GitHub Actions Linting Status](https://github.com/nf-core/cutandrun/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/cutandrun/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/cutandrun/results)
		[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
		[![DOI](http://img.shields.io/badge/DOI-10.5281/zenodo.5653535-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5653535)

		[![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/)
		@@ -92,8 +92,7 @@ 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/cutandrun 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/cutandrun for your analysis, please cite it using the following doi: [10.5281/zenodo.5653535](https://doi.org/10.5281/zenodo.5653535)

		An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

lib/WorkflowMain.groovy

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		@@ -9,9 +9,7 @@ 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" +
		" https://doi.org/10.5281/zenodo.5653535\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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