diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1aad7ad7..3d48b275 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#134](https://github.com/nf-core/bacass/pull/134) - Fixed samples reported of prokka/bakta in multiqc report.
+
 - [#125](https://github.com/nf-core/bacass/pull/125) - Fixed conflicting settings in save_trimmed_fail parameter.
 
 ### `Dependencies`
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 32c030f0..e647ad5a 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -13,3 +13,6 @@ report_section_order:
 export_plots: true
 
 disable_version_detection: true
+use_filename_as_sample_name:
+  - prokka
+  - bakta
diff --git a/workflows/bacass.nf b/workflows/bacass.nf
index fa633ce5..076e62c2 100644
--- a/workflows/bacass.nf
+++ b/workflows/bacass.nf
@@ -413,7 +413,7 @@ workflow BACASS {
             [],
             []
         )
-        ch_prokka_txt_multiqc   = PROKKA.out.txt.collect()
+        ch_prokka_txt_multiqc   = PROKKA.out.txt.map{ meta, prokka_txt -> [ prokka_txt ]}
         ch_versions             = ch_versions.mix(PROKKA.out.versions)
     }
 
@@ -432,7 +432,7 @@ workflow BACASS {
             params.baktadb,
             params.baktadb_download
         )
-        ch_bakta_txt_multiqc    = BAKTA_DBDOWNLOAD_RUN.out.bakta_txt_multiqc.collect()
+        ch_bakta_txt_multiqc    = BAKTA_DBDOWNLOAD_RUN.out.bakta_txt_multiqc.map{ meta, bakta_txt -> [ bakta_txt ]}
         ch_versions             = ch_versions.mix(BAKTA_DBDOWNLOAD_RUN.out.versions)
     }
     //
@@ -478,8 +478,8 @@ workflow BACASS {
     ch_multiqc_files                      = ch_multiqc_files.mix(ch_kraken_short_multiqc.collect{it[1]}.ifEmpty([]))
     ch_multiqc_files                      = ch_multiqc_files.mix(ch_kraken_long_multiqc.collect{it[1]}.ifEmpty([]))
     ch_multiqc_files                      = ch_multiqc_files.mix(ch_quast_multiqc.collect{it[1]}.ifEmpty([]))
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_prokka_txt_multiqc.collect{it[1]}.ifEmpty([]))
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_bakta_txt_multiqc.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(ch_prokka_txt_multiqc.collect().ifEmpty([]))
+    ch_multiqc_files                      = ch_multiqc_files.mix(ch_bakta_txt_multiqc.collect().ifEmpty([]))
     ch_multiqc_files                      = ch_multiqc_files.mix(ch_nanoplot_txt_multiqc.collect{it[1]}.ifEmpty([]))
     ch_multiqc_files                      = ch_multiqc_files.mix(ch_porechop_log_multiqc.collect{it[1]}.ifEmpty([]))
     ch_multiqc_files                      = ch_multiqc_files.mix(ch_pycoqc_multiqc.collect{it[1]}.ifEmpty([]))