diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5019c34f2..9c7743649 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,18 @@
 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).
 
+# 3.18.1 - 2024-03-24
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Milos Micik](https://github.com/milos7250)
+
+### Enhancements & fixes
+
+- [PR #1526](https://github.com/nf-core/rnaseq/pull/1526) - Fix naming of GFFREAD outputs (`null.gtf`).
+
 # 3.18.0 - 2024-12-19
 
 ### Credits
diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index c1b8b4c66..a3bef1ceb 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -92,7 +92,8 @@ workflow PREPARE_GENOME {
                 ch_gff      = GUNZIP_GFF ( [ [:], file(gff, checkIfExists: true) ] ).gunzip
                 ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions)
             } else {
-                ch_gff = Channel.value(file(gff, checkIfExists: true)).map { [ [:], it ] }
+                gff_file = file(gff, checkIfExists: true)
+                ch_gff   = Channel.value( gff_file ).map { [ ['id': "${gff_file.baseName}"], it ] }
             }
             ch_gtf      = GFFREAD ( ch_gff, [] ).gtf.map { it[1] }
             ch_versions = ch_versions.mix(GFFREAD.out.versions)