diff --git a/modules/local/collect_featurecounts.nf b/modules/local/collect_featurecounts.nf
index d4de1ec7..bbb7cb90 100644
--- a/modules/local/collect_featurecounts.nf
+++ b/modules/local/collect_featurecounts.nf
@@ -54,7 +54,7 @@ process COLLECT_FEATURECOUNTS {
         ) %>%
         tidyr::unnest(d) %>%
         select(-f) %>%
-        write_tsv("${prefix}_counts.tsv.gz")
+        write_tsv("magmap.${prefix}.counts.tsv.gz")
 
         writeLines(c("\\"${task.process}\\":", paste0("    R: ", paste0(R.Version()[c("major","minor")], collapse = ".")), paste0("    dplyr: ", packageVersion('dplyr')),
             paste0("    dtplyr: ", packageVersion('dtplyr')), paste0("    data.table: ", packageVersion('data.table')) ), "versions.yml")
diff --git a/modules/local/prokkagff2tsv.nf b/modules/local/prokkagff2tsv.nf
index b8735162..f298a5bc 100644
--- a/modules/local/prokkagff2tsv.nf
+++ b/modules/local/prokkagff2tsv.nf
@@ -44,7 +44,7 @@ process PROKKAGFF2TSV {
         relocate(sort(colnames(.)[8:ncol(.)]), .after = 7) %>%
         relocate(orf) %>%
         as.data.table() %>%
-        write_tsv("${prefix}.prokka-annotations.tsv.gz")
+        write_tsv("magmap.${prefix}.prokka-annotations.tsv.gz")
 
     writeLines(
         c(
diff --git a/workflows/magmap.nf b/workflows/magmap.nf
index 8456deb0..ba1ced72 100644
--- a/workflows/magmap.nf
+++ b/workflows/magmap.nf
@@ -508,7 +508,7 @@ workflow MAGMAP {
 
         ch_header
             .concat( ch_metadata )
-            .collectFile(name: "summary_table.taxonomy.tsv",
+            .collectFile(name: "magmap.summary_table.taxonomy.tsv",
             newLine: true,
             storeDir: "${params.outdir}/summary_tables")
     }