diff --git a/conf/modules.config b/conf/modules.config
index 9638ac28..be46ebd7 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -141,7 +141,7 @@ process {
 
     withName: EXTRACT_ANNOTATION_STATISTICS_INFO {
         publishDir = [
-            path: { "${params.outdir}/annotation_stats" },
+            path: { "${params.outdir}/gene" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
diff --git a/docs/output.md b/docs/output.md
index fbedfe78..4920f6d5 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -53,7 +53,7 @@ This pipeline can generate some statistics using AGAT and a BUSCO completeness s
 <detail markdown="1">
 <summary>Output files</summary>
 
-- `annotation_stats/` -`<gca_accession>_annotation.csv`: collated annotation statistics file
+- `gene/` -`<annotation_input_filename>_stats.csv`: collated annotation statistics file
 
 </details>
 
diff --git a/modules/local/extract_annotation_statistics_info.nf b/modules/local/extract_annotation_statistics_info.nf
index 054c93b3..f87bfd1f 100644
--- a/modules/local/extract_annotation_statistics_info.nf
+++ b/modules/local/extract_annotation_statistics_info.nf
@@ -19,8 +19,8 @@ process EXTRACT_ANNOTATION_STATISTICS_INFO{
     task.ext.when == null || task.ext.when
 
     script:
-    def prefix = task.ext.prefix ?: meta.id
-    def output_file = "${prefix}.csv"
+    def prefix = task.ext.prefix ?: meta.filename
+    def output_file = "${prefix}.stats.csv"
     """
 
     extract_annotation_statistics_info.py \\
diff --git a/subworkflows/local/annotation_statistics.nf b/subworkflows/local/annotation_statistics.nf
index 4b596a5c..41ab6c42 100644
--- a/subworkflows/local/annotation_statistics.nf
+++ b/subworkflows/local/annotation_statistics.nf
@@ -23,7 +23,7 @@ workflow ANNOTATION_STATISTICS {
     // Map the GFF channel to create a tuple with metadata and the file
     gff
     | map { file -> 
-        [ [ 'id': params.assembly + '_annotation', 'ext': "gff" ], file ]
+        [ [ 'id': params.assembly + '_annotation', 'ext': "gff", 'filename': file.baseName ], file ]
     }
     | set { ch_gff_tupple }