diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8304e66b..f95e352d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -26,6 +26,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | Porechop_ABI |                  | 0.5.0       |
 | Filtlong     | 0.2.0            | 0.2.1       |
 
+### `Deprecated`
+
 ## 3.1.0 [2024-10-04]
 
 ### `Added`
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index fa0f9b32..fe8d388f 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/mag/releases/tag/3.1.0" target="_blank">nf-core/mag</a>
+  This report has been generated by the <a href="https://github.com/nf-core/mag/tree/dev" target="_blank">nf-core/mag</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/mag/3.1.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/mag/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mag-methods-description":
     order: -1000
diff --git a/docs/images/mag_workflow.png b/docs/images/mag_workflow.png
index ee68d126..4c99e66b 100644
Binary files a/docs/images/mag_workflow.png and b/docs/images/mag_workflow.png differ
diff --git a/docs/images/mag_workflow.svg b/docs/images/mag_workflow.svg
index 4113143c..b3434968 100644
--- a/docs/images/mag_workflow.svg
+++ b/docs/images/mag_workflow.svg
@@ -352,7 +352,7 @@
      inkscape:pageshadow="2"
      inkscape:zoom="0.94128294"
      inkscape:cx="640.61503"
-     inkscape:cy="418.04646"
+     inkscape:cy="418.57765"
      inkscape:document-units="mm"
      inkscape:current-layer="g6248"
      showgrid="true"
@@ -2299,7 +2299,7 @@
            id="tspan3824"
            style="font-style:normal;font-variant:normal;font-weight:bold;font-stretch:normal;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro Bold';stroke-width:0.264583"
            x="265.54773"
-           y="66.962173">v3.0</tspan></text><g
+           y="66.962173">v3.1</tspan></text><g
          id="g1307"
          transform="translate(3.3065026,127.42992)"><text
            xml:space="preserve"
diff --git a/nextflow.config b/nextflow.config
index c0284ce6..15dc2d53 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -393,7 +393,7 @@ manifest {
     description     = """Assembly, binning and annotation of metagenomes"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '3.1.0'
+    version         = 'dev'
     doi             = '10.1093/nargab/lqac007'
 }