Add missing CHANGELOG entry and bump versions for release

CHANGELOG.md

@@ -3,16 +3,22 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## dev [unreleased]
+## 3.0.1 [2024-06-06]
 
 ### `Added`
 
 ### `Changed`
 
 ### `Fixed`
 
+- [#618](https://github.com/nf-core/mag/pull/618) - Fix CENTRIFUGE mkfifo failures by using work directory /tmp (reported by @skrakau, fix by @jfy133)
+
 ### `Dependencies`
 
+| Tool       | Previous version | New version |
+| ---------- | ---------------- | ----------- |
+| Centrifuge | 1.0.4_beta       | 1.0.4.1     |
+
 ### `Deprecated`
 
 ## 3.0.0 - [2024-05-13]

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/tree/dev" target="_blank">nf-core/mag</a>
+  This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/3.0.1" 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/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/mag/3.0.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mag-methods-description":
     order: -1000

nextflow.config

@@ -390,7 +390,7 @@ manifest {
     description     = """Assembly, binning and annotation of metagenomes"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '3.0.1dev'
+    version         = '3.0.1'
     doi             = '10.1093/nargab/lqac007'
 }