From 38a818fd174718229385a0ed301c42c76cadb9ec Mon Sep 17 00:00:00 2001
From: sofstam <sofia.stamouli@scilifelab.se>
Date: Thu, 1 Dec 2022 13:42:21 +0100
Subject: [PATCH] Apply review suggestions

---
 conf/modules.config    |  6 +++---
 conf/test_motus.config |  6 +++---
 nextflow.config        |  8 ++++----
 nextflow_schema.json   | 28 +++++++++++++++-------------
 4 files changed, 25 insertions(+), 23 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 1ff6f55..43e179d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -448,9 +448,9 @@ process {
     withName: MOTUS_PROFILE {
         ext.args = {
             [
-                params.motus_use_ncbi_ids ? "-p" : "",
-                params.motus_output_type ? "-c" : "",
-                params.motus_save_mgcreadcounts ?  "-M ${task.ext.prefix}.mgc" : ""
+                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}" }
diff --git a/conf/test_motus.config b/conf/test_motus.config
index b5c2c51..92c9a91 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
-    motus_save_mgcreadcounts              = true
-    motus_use_ncbi_ids                    = true
-    motus_output_type                     = true
+    motus_save_mgc_read_counts            = true
+    motus_remove_ncbi_ids                 = true
+    motus_use_relative_abundance          = true
     run_profile_standardisation           = true
 }
diff --git a/nextflow.config b/nextflow.config
index b1da76a..84c5242 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -139,10 +139,10 @@ 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
-    motus_output_type          = false
-    motus_use_ncbi_ids         = false
-    motus_save_mgcreadcounts   = 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 2864a52..e6db686 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -472,18 +472,6 @@
                     "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_ncbi_ids": {
-                    "type": "boolean",
-                    "description": "Turn on printing ncbi taxonomic ids."
-                },
-                "motus_save_mgcreadcounts": {
-                    "type": "boolean",
-                    "description": "Turn on saving the mgc reads count to a separate file."
-                },
-                "motus_output_type": {
-                    "type": "boolean",
-                    "description": "Turn on printing result as counts instead of relative abundances."
                 }
             },
             "fa_icon": "fas fa-align-center"
@@ -783,5 +771,19 @@
         {
             "$ref": "#/definitions/reference_genome_options"
         }
-    ]
+    ],
+    "properties": {
+        "motus_use_relative_abundance": {
+            "type": "string",
+            "default": "false"
+        },
+        "motus_remove_ncbi_ids": {
+            "type": "string",
+            "default": "false"
+        },
+        "motus_save_mgc_read_counts": {
+            "type": "string",
+            "default": "false"
+        }
+    }
 }