diff --git a/modules.json b/modules.json
index cbbae85..7c02b3e 100644
--- a/modules.json
+++ b/modules.json
@@ -96,11 +96,11 @@
                 },
                 "metaphlan3/mergemetaphlantables": {
                     "branch": "master",
-                    "git_sha": "940d7fe9d63962e0e2ba0987e2893fb0aff832e3"
+                    "git_sha": "36bcd675ae76a379a38165898a203f4915823f4f"
                 },
                 "metaphlan3/metaphlan3": {
                     "branch": "master",
-                    "git_sha": "940d7fe9d63962e0e2ba0987e2893fb0aff832e3"
+                    "git_sha": "978087354eb72ac1f6e18a3f790fad9bc4d05840"
                 },
                 "minimap2/align": {
                     "branch": "master",
diff --git a/modules/nf-core/modules/metaphlan3/mergemetaphlantables/main.nf b/modules/nf-core/modules/metaphlan3/mergemetaphlantables/main.nf
index 6fd05e3..7c37eca 100644
--- a/modules/nf-core/modules/metaphlan3/mergemetaphlantables/main.nf
+++ b/modules/nf-core/modules/metaphlan3/mergemetaphlantables/main.nf
@@ -7,10 +7,10 @@ process METAPHLAN3_MERGEMETAPHLANTABLES {
         'quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0' }"
 
     input:
-    path(profiles)
+    tuple val(meta), path(profiles)
 
     output:
-    tuple path("${prefix}.txt") , emit: txt
+    tuple val(meta), path("${prefix}.txt") , emit: txt
     path "versions.yml" , emit: versions
 
     when:
@@ -18,7 +18,7 @@ process METAPHLAN3_MERGEMETAPHLANTABLES {
 
     script:
     def args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: "merged_abundance_table"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     merge_metaphlan_tables.py \\
         $args \\
diff --git a/modules/nf-core/modules/metaphlan3/mergemetaphlantables/meta.yml b/modules/nf-core/modules/metaphlan3/mergemetaphlantables/meta.yml
index c94be25..365973e 100644
--- a/modules/nf-core/modules/metaphlan3/mergemetaphlantables/meta.yml
+++ b/modules/nf-core/modules/metaphlan3/mergemetaphlantables/meta.yml
@@ -15,12 +15,22 @@ tools:
       licence: ["MIT License"]
 
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - profiles:
       type: file
       description: List of per-sample MetaPhlAn3 taxonomic abundance tables
       pattern: "*"
 
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/nf-core/modules/metaphlan3/metaphlan3/main.nf b/modules/nf-core/modules/metaphlan3/metaphlan3/main.nf
index e56f102..1453466 100644
--- a/modules/nf-core/modules/metaphlan3/metaphlan3/main.nf
+++ b/modules/nf-core/modules/metaphlan3/metaphlan3/main.nf
@@ -1,4 +1,4 @@
-process METAPHLAN3 {
+process METAPHLAN3_METAPHLAN3 {
     tag "$meta.id"
     label 'process_high'
 
diff --git a/modules/nf-core/modules/metaphlan3/metaphlan3/meta.yml b/modules/nf-core/modules/metaphlan3/metaphlan3/meta.yml
index 093de5b..659d83a 100644
--- a/modules/nf-core/modules/metaphlan3/metaphlan3/meta.yml
+++ b/modules/nf-core/modules/metaphlan3/metaphlan3/meta.yml
@@ -1,4 +1,4 @@
-name: metaphlan3
+name: metaphlan3_metaphlan3
 description: MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
 keywords:
   - metagenomics
diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
index 37b4a2c..c2ef508 100644
--- a/subworkflows/local/profiling.nf
+++ b/subworkflows/local/profiling.nf
@@ -7,7 +7,7 @@ include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV  } from '../../modules/nf-core/mo
 include { KRAKEN2_KRAKEN2                       } from '../../modules/nf-core/modules/kraken2/kraken2/main'
 include { CENTRIFUGE_CENTRIFUGE                 } from '../../modules/nf-core/modules/centrifuge/centrifuge/main'
 include { CENTRIFUGE_KREPORT                    } from '../../modules/nf-core/modules/centrifuge/kreport/main'
-include { METAPHLAN3                            } from '../../modules/nf-core/modules/metaphlan3/metaphlan3/main'
+include { METAPHLAN3_METAPHLAN3                 } from '../../modules/nf-core/modules/metaphlan3/metaphlan3/main'
 include { KAIJU_KAIJU                           } from '../../modules/nf-core/modules/kaiju/kaiju/main'
 include { DIAMOND_BLASTX                        } from '../../modules/nf-core/modules/diamond/blastx/main'
 include { MOTUS_PROFILE                         } from '../../modules/nf-core/modules/motus/profile/main'
@@ -168,9 +168,9 @@ workflow PROFILING {
                                     db: it[3]
                             }
 
-        METAPHLAN3 ( ch_input_for_metaphlan3.reads, ch_input_for_metaphlan3.db )
-        ch_versions        = ch_versions.mix( METAPHLAN3.out.versions.first() )
-        ch_raw_profiles    = ch_raw_profiles.mix( METAPHLAN3.out.biom )
+        METAPHLAN3_METAPHLAN3 ( ch_input_for_metaphlan3.reads, ch_input_for_metaphlan3.db )
+        ch_versions        = ch_versions.mix( METAPHLAN3_METAPHLAN3.out.versions.first() )
+        ch_raw_profiles    = ch_raw_profiles.mix( METAPHLAN3_METAPHLAN3.out.profile )
 
     }
 
diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf
index 6d404be..a557bff 100644
--- a/subworkflows/local/standardisation_profiles.nf
+++ b/subworkflows/local/standardisation_profiles.nf
@@ -65,7 +65,7 @@ workflow STANDARDISATION_PROFILES {
                             .map { [it[0]['db_name'], it[1]] }
                             .groupTuple()
                             .map {
-                                [it[1]]
+                                [[id:it[0]], it[1]]
                             }
 
     METAPHLAN3_MERGEMETAPHLANTABLES ( ch_profiles_for_metaphlan3 )