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 ff8ba10a..dfb6d8bd 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -260,7 +260,7 @@ manifest {
     description     = """Pipeline to run and benchmark multiple sequence alignment tools."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.1'
-    version         = '1.0.0'
+    version         = '1.1.0dev'
     doi             = 'https://doi.org/10.5281/zenodo.13889386'
 }