diff --git a/README.md b/README.md
index 42f5fecc..73d24581 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@
 <!--[![GitHub Actions CI Status](https://github.com/sanger-tol/blobtoolkit/workflows/nf-core%20CI/badge.svg)](https://github.com/sanger-tol/blobtoolkit/actions?query=workflow%3A%22nf-core+CI%22)-->
 
 [![GitHub Actions Linting Status](https://github.com/sanger-tol/blobtoolkit/workflows/nf-core%20linting/badge.svg)](https://github.com/sanger-tol/blobtoolkit/actions?query=workflow%3A%22nf-core+linting%22)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7949058-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7949058)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.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/)
@@ -107,7 +107,7 @@ If you would like to contribute to this pipeline, please see the [contributing g
 
 <!-- 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 sanger-tol/blobtoolkit for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+If you use sanger-tol/blobtoolkit for your analysis, please cite it using the following doi: [10.5281/zenodo.7949058](https://doi.org/10.5281/zenodo.7949058)
 
 <!-- Add bibliography of tools and data used in your pipeline -->
 
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index c3b0de0e..53b29a95 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -13,7 +13,7 @@ class WorkflowMain {
         return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
             // 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.7949058\n\n" +
             "* The nf-core framework\n" +
             "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
             "* Software dependencies\n" +
diff --git a/nextflow.config b/nextflow.config
index fa9e2065..63997fbc 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -222,7 +222,7 @@ manifest {
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
     version         = '0.1.0'
-    doi             = '10.5281/zenodo.XXXXXXX'
+    doi             = '10.5281/zenodo.7949058'
 }
 
 // Load modules.config for DSL2 module specific options