diff --git a/README.md b/README.md
index 149ce89d..60996b97 100644
--- a/README.md
+++ b/README.md
@@ -6,7 +6,7 @@
 </h1>
 
 [![GitHub Actions CI Status](https://github.com/nf-core/multiplesequencealign/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/multiplesequencealign/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/nf-core/multiplesequencealign/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/multiplesequencealign/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/multiplesequencealign/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/multiplesequencealign/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/multiplesequencealign/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/multiplesequencealign/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.13889386-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.13889386)
 [![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/)
@@ -123,8 +123,7 @@ 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/multiplesequencealign 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/multiplesequencealign for your analysis, please cite it using the following doi: [10.5281/zenodo.13889386](https://doi.org/10.5281/zenodo.13889386)
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 6029e88f..98965b3c 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/multiplesequencealign/releases/tag/1.0.0" target="_blank">nf-core/multiplesequencealign</a>
+  This report has been generated by the <a href="https://github.com/nf-core/multiplesequencealign/tree/dev" target="_blank">nf-core/multiplesequencealign</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/multiplesequencealign/1.0.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/multiplesequencealign/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-multiplesequencealign-methods-description":
     order: -1000
diff --git a/nextflow.config b/nextflow.config
index eabe79d5..f239efec 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -256,8 +256,8 @@ manifest {
     description     = """Pipeline to run and benchmark multiple sequence alignment tools."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '1.0.0'
-    doi             = ''
+    version         = '1.1.0dev'
+    doi             = 'https://doi.org/10.5281/zenodo.13889386'
 }
 
 // Nextflow plugins