diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1a482e93..25e747be 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#296](https://github.com/nf-core/funcscan/pull/296) Fixed empty output when saving prodigal annotations. (reported by @louperelo, fix by @jasmezz)
+
 ### `Dependencies`
 
 ### `Deprecated`
diff --git a/conf/modules.config b/conf/modules.config
index 02f2ea53..be7009d8 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -130,7 +130,7 @@ process {
             path: { "${params.outdir}/annotation/prodigal/${meta.id}" },
             mode: params.publish_dir_mode,
             enabled: params.save_annotations,
-            pattern: "*.{faa,fna,gff}",
+            pattern: "*.{faa,fna,gff}.gz",
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
         ext.args = [
@@ -146,7 +146,7 @@ process {
             path: { "${params.outdir}/annotation/prodigal/${meta.id}" },
             mode: params.publish_dir_mode,
             enabled: params.save_annotations,
-            pattern: "*.gbk",
+            pattern: "*.gbk.gz",
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
         ext.args = [