diff --git a/conf/modules.config b/conf/modules.config
index 4f0181d..f6045e5 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -457,6 +457,13 @@ process {
     }
 
     withName: MOTUS_PROFILE {
+        ext.args = {
+            [
+                params.motus_remove_ncbi_ids ? "" : "-p",
+                params.motus_use_relative_abundance ? "" : "-c",
+                params.motus_save_mgc_read_counts ?  "-M ${task.ext.prefix}.mgc" : ""
+            ].join(',').replaceAll(','," ")
+            }
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/motus/${meta.db_name}/" },
diff --git a/conf/test_motus.config b/conf/test_motus.config
index a077dad..ee41447 100644
--- a/conf/test_motus.config
+++ b/conf/test_motus.config
@@ -44,5 +44,8 @@ params {
     run_diamond                           = false
     run_krakenuniq                        = false
     run_motus                             = true
+    motus_save_mgc_read_counts            = false
+    motus_remove_ncbi_ids                 = false
+    motus_use_relative_abundance          = false
     run_profile_standardisation           = true
 }
diff --git a/nextflow.config b/nextflow.config
index 721a21c..3cf160d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -145,7 +145,10 @@ params {
     diamond_save_reads         = false // this will override default diamond output format so no taxonomic profile is generated! added directly to module in profiling.nf
 
     // mOTUs
-    run_motus                  = false
+    run_motus                       = false
+    motus_use_relative_abundance    = false
+    motus_remove_ncbi_ids           = false
+    motus_save_mgc_read_counts      = false
 
     // krona
     run_krona                  = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 28d5446..ae4e311 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -464,6 +464,18 @@
                     "type": "boolean",
                     "fa_icon": "fas fa-toggle-on",
                     "description": "Turn on profiling with mOTUs. Requires database to be present CSV file passed to --databases"
+                },
+                "motus_use_relative_abundance": {
+                    "type": "boolean",
+                    "description": "Turn on printing relative abundance instead of counts."
+                },
+                "motus_save_mgc_read_counts": {
+                    "type": "boolean",
+                    "description": "Turn on saving the mgc reads count."
+                },
+                "motus_remove_ncbi_ids": {
+                    "type": "boolean",
+                    "description": "Turn on removing NCBI taxonomic IDs."
                 }
             },
             "fa_icon": "fas fa-align-center"