diff --git a/conf/modules.config b/conf/modules.config
index 0f54301..63be9ff 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -448,9 +448,9 @@ process {
     withName: MOTUS_PROFILE {
         ext.args = {
             [
-                params.save_ncbi_id ? "-p" : "",
-                params.save_read_counts ? "-c" : "",
-                params.save_mgc_counts ?  "-M ${task.ext.prefix}.mgc" : ""
+                params.motus_ncbi_id ? "-p" : "",
+                params.motus_read_counts ? "-c" : "",
+                params.motus_mgc_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}" }
diff --git a/conf/test_motus.config b/conf/test_motus.config
index 70681dd..8eb324b 100644
--- a/conf/test_motus.config
+++ b/conf/test_motus.config
@@ -39,8 +39,8 @@ params {
     run_centrifuge                        = false
     run_diamond                           = false
     run_motus                             = true
-    save_mgc_counts                       = true
-    save_ncbi_id                          = true
-    save_read_counts                      = true
+    motus_mgc_counts                       = true
+    motus_ncbi_id                          = true
+    motus_read_counts                      = true
     run_profile_standardisation           = true
 }
diff --git a/nextflow.config b/nextflow.config
index 91875b2..c9bb0f4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -140,9 +140,9 @@ params {
 
     // mOTUs
     run_motus                  = false
-    save_mgc_counts            = false
-    save_ncbi_id               = false
-    save_read_counts           = false
+    motus_mgc_counts            = false
+    motus_ncbi_id               = false
+    motus_read_counts           = false
 
     // krona
     run_krona                  = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index cec0ab7..0b20762 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -63,7 +63,10 @@
                 "preprocessing_qc_tool": {
                     "type": "string",
                     "default": "fastqc",
-                    "enum": ["fastqc", "falco"],
+                    "enum": [
+                        "fastqc",
+                        "falco"
+                    ],
                     "help_text": "Falco is designed as a drop-in replacement for FastQC but written in C++ for faster computation. We particularly recommend using falco when using long reads (due to reduced memory constraints), however is also applicable for short reads.",
                     "description": "Specify the tool used for quality control of raw sequencing reads",
                     "fa_icon": "fas fa-tools"
@@ -470,17 +473,17 @@
                     "fa_icon": "fas fa-toggle-on",
                     "description": "Turn on profiling with mOTUs. Requires database to be present CSV file passed to --databases"
                 },
-                "save_mgc_counts": {
+                "motus_mgc_counts": {
                     "type": "boolean",
-                    "description": "Save the mgc reads count for mOTUs."
+                    "description": "Save the mgc reads count."
                 },
-                "save_read_counts": {
+                "motus_ncbi_id": {
                     "type": "boolean",
-                    "description": "Print mOTUs result as counts instead of relative abundances."
+                    "description": "Print NCBI id."
                 },
-                "save_ncbi_id": {
+                "motus_read_counts": {
                     "type": "boolean",
-                    "description": "Print NCBI taxonomic id for mOTUs."
+                    "description": "Print result as counts instead of relative abundances."
                 }
             },
             "fa_icon": "fas fa-align-center"
@@ -653,16 +656,6 @@
                     "fa_icon": "fas fa-file-upload",
                     "hidden": true
                 },
-                "preprocessing_qc_tool": {
-                    "type": "string",
-                    "default": "fastqc",
-                    "enum": [
-                        "fastqc",
-                        "falco"
-                    ],
-                    "help_text": "Falco is designed as a drop-in replacement for FastQC but written in C++ for faster computation. We particularly recommend using falco when using long reads (due to reduced memory constraints), however is also applicable for short reads.",
-                    "description": "Specify the tool used for quality control of raw sequencing reads"
-                },
                 "monochrome_logs": {
                     "type": "boolean",
                     "description": "Do not use coloured log outputs.",
@@ -791,4 +784,4 @@
             "$ref": "#/definitions/reference_genome_options"
         }
     ]
-}
\ No newline at end of file
+}