diff --git a/conf/modules.config b/conf/modules.config
index f64c423..6099422 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -427,6 +427,8 @@ process {
     }
 
     withName: MOTUS_MERGE {
+        ext.args = { params.generate_biom_output ? "-B" : "" }
+        ext.prefix = { "motus_${meta.id}_combined_reports" }
         publishDir = [
             path: { "${params.outdir}/motus/" },
             mode: params.publish_dir_mode
diff --git a/modules.json b/modules.json
index 0634112..f174b6f 100644
--- a/modules.json
+++ b/modules.json
@@ -115,7 +115,7 @@
                 },
                 "motus/merge": {
                     "branch": "master",
-                    "git_sha": "b02e648c221e1da17cb589eefe297e61ec9e9c49"
+                    "git_sha": "54ff289487244bf15543ecfa62bd4df49be72b73"
                 },
                 "motus/profile": {
                     "branch": "master",
diff --git a/modules/nf-core/modules/motus/merge/main.nf b/modules/nf-core/modules/motus/merge/main.nf
index 01ca5a2..a050c7a 100644
--- a/modules/nf-core/modules/motus/merge/main.nf
+++ b/modules/nf-core/modules/motus/merge/main.nf
@@ -1,6 +1,7 @@
 VERSION = '3.0.1'
 
 process MOTUS_MERGE {
+    tag "$meta.id"
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
@@ -9,14 +10,13 @@ process MOTUS_MERGE {
         'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
 
     input:
-    path input
+    tuple val(meta), path(input)
     path db // to stop docker saying it can't find it... would have to have the module in upstream steps anyway
     path profile_version_yml, stageAs: 'profile_version.yml'
-    val biom_format
 
     output:
-    path("*.txt") , optional: true, emit: txt
-    path("*.biom"), optional: true, emit: biom
+    tuple val(meta), path("*.txt") , optional: true, emit: txt
+    tuple val(meta), path("*.biom"), optional: true, emit: biom
     path "versions.yml" , emit: versions
 
     when:
@@ -24,16 +24,16 @@ process MOTUS_MERGE {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = 'motus_merged'
+    def prefix = task.ext.prefix ?: "${meta.id}"
     def cmd_input = input.size() > 1 ? "-i ${input.join(',')}" : input.isDirectory() ? "-d ${input}" : "-i ${input}"
-    def output = biom_format ? "-B -o ${prefix}.biom" : "-o ${prefix}.txt"
+    def suffix = task.ext.args?.contains("-B") ? "biom" : "txt"
     """
     motus \\
         merge \\
         -db $db \\
         ${cmd_input} \\
         $args \\
-        ${output}
+        -o ${prefix}.${suffix}
 
     ## Take version from the mOTUs/profile module output, as cannot reconstruct
     ## version without having database staged in this directory.
diff --git a/modules/nf-core/modules/motus/merge/meta.yml b/modules/nf-core/modules/motus/merge/meta.yml
index c9c7711..02d11d0 100644
--- a/modules/nf-core/modules/motus/merge/meta.yml
+++ b/modules/nf-core/modules/motus/merge/meta.yml
@@ -35,9 +35,6 @@ input:
         this itself without having the motus database present and configured with the tool
         so here we take it from what is already reported by the upstream module.
       pattern: "versions.yml"
-  - biom_format:
-      type: boolean
-      description: Whether to save output OTU table in biom format
 
 output:
   - versions:
diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf
index c8c364d..7a441ff 100644
--- a/subworkflows/local/standardisation_profiles.nf
+++ b/subworkflows/local/standardisation_profiles.nf
@@ -117,7 +117,16 @@ workflow STANDARDISATION_PROFILES {
     // mOTUs has a 'single' database, and cannot create custom ones.
     // Therefore removing db info here, and publish merged at root mOTUs results
     // directory
-    MOTUS_MERGE ( ch_input_profiles.motus.map{it[1]}.collect(), ch_input_databases.motus.map{it[1]}, motu_version, params.generate_biom_output )
+
+    ch_profiles_for_motus = ch_input_profiles.motus
+                                .map { [it[0]['db_name'], it[1]] }
+                                .groupTuple()
+                                .map {
+                                    [[id:it[0]], it[1]]
+                                }
+
+    MOTUS_MERGE ( ch_profiles_for_motus, ch_input_databases.motus.map{it[1]}, motu_version )
+
     if ( params.generate_biom_output ) {
         ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.biom )
     } else {