diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 5e0f10e0..44a9684d 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/rnafusion/2.4.0" target="_blank">nf-core/rnafusion</a>
+  This report has been generated by the <a href="https://github.com/nf-core/rnafusion/3.0.0dev" target="_blank">nf-core/rnafusion</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/rnafusion/2.4.0/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/rnafusion/3.0.0dev/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-rnafusion-methods-description":
     order: -1000
diff --git a/nextflow.config b/nextflow.config
index 994e96e3..909edafe 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -295,7 +295,7 @@ manifest {
     description     = """Nextflow rnafusion analysis pipeline, part of the nf-core community."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version = '2.4.0'
+    version = '3.0.0dev'
     doi             = ''
 }