Merge branch 'master' into merging-template-updates

README.md

@@ -8,7 +8,7 @@
 **Multi-step pipeline dedicated to genetic imputation from simulation to validation**
 
 [![GitHub Actions CI Status](https://github.com/nf-core/phaseimpute/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml) [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/phaseimpute/results) [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
+[![GitHub Actions Linting Status](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/phaseimpute/actions/workflows/linting.yml) [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/phaseimpute/results) [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14329225-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14329225) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](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/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
@@ -111,7 +111,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 <!-- 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/phaseimpute 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/phaseimpute for your analysis, please cite it using the following doi: [10.5281/zenodo.14329225](https://doi.org/10.5281/zenodo.14329225)
 
 An extensive list of references for the tools used by the pipeline, including QUILT, GLIMPSE, and STITCH, can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 

nextflow.config

@@ -332,7 +332,7 @@ manifest {
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
     version         = '1.1.0dev'
-    doi             = ''
+    doi             = 'https://doi.org/10.5281/zenodo.14329225'
 }
 
 // Nextflow plugins