diff --git a/assets/nf-params.yml b/assets/nf-params.yml
index 995f2130..51a7ab6b 100644
--- a/assets/nf-params.yml
+++ b/assets/nf-params.yml
@@ -107,7 +107,7 @@
 ##     Remove duplicated reads (exact same sequence)
 ##     Type: boolean
 ## -----------------------------------------------------------------------------
-# dedup = false
+# dedup = null
 
 ## -----------------------------------------------------------------------------
 ## remove_polyg
@@ -115,7 +115,7 @@
 ##     Remove PolyG sequences (length of 10 or more)
 ##     Type: boolean
 ## -----------------------------------------------------------------------------
-# remove_polyg = false
+# remove_polyg = null
 
 
 ## =============================================================================
@@ -271,7 +271,7 @@
 ##     Skip analysis step
 ##     Type: boolean
 ## -----------------------------------------------------------------------------
-# skip_analysis = false
+# skip_analysis = null
 
 ## -----------------------------------------------------------------------------
 ## compute_polarization
@@ -296,7 +296,7 @@
 ##     computing polarization, coabundance and colocalization scores
 ##     Type: boolean
 ## -----------------------------------------------------------------------------
-# use_full_bipartite = false
+# use_full_bipartite = null
 
 ## -----------------------------------------------------------------------------
 ## polarization_normalization
@@ -313,7 +313,7 @@
 ##     polarization
 ##     Type: boolean
 ## -----------------------------------------------------------------------------
-# polarization_binarization = false
+# polarization_binarization = null
 
 ## -----------------------------------------------------------------------------
 ## colocalization_transformation
@@ -362,7 +362,7 @@
 ##     Skip report generation
 ##     Type: boolean
 ## -----------------------------------------------------------------------------
-# skip_report = false
+# skip_report = null
 
 
 ## =============================================================================
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3210d63f..60ac0bc3 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -90,19 +90,18 @@
                 "dedup": {
                     "fa_icon": "fas clone",
                     "description": "Remove duplicated reads (exact same sequence)",
-                    "type": "boolean",
-                    "default": false
+                    "type": "boolean"
                 },
                 "remove_polyg": {
                     "fa_icon": "fas g",
                     "description": "Remove PolyG sequences (length of 10 or more)",
-                    "type": "boolean",
-                    "default": false
+                    "type": "boolean"
                 }
             }
         },
         "adapterqc_options": {
             "title": "Adapter QC Options",
+            "type": "object",
             "properties": {
                 "adapterqc_mismatches": {
                     "fa_icon": "fas not-equal",
@@ -116,6 +115,7 @@
         },
         "demux_options": {
             "title": "Demux options",
+            "type": "object",
             "properties": {
                 "demux_mismatches": {
                     "fa_icon": "fas not-equal",
@@ -135,9 +135,10 @@
         },
         "collapse_options": {
             "title": "Collapse options",
+            "type": "object",
             "properties": {
                 "markers_ignore": {
-                    "fa-icon": "fas fa-list",
+                    "fa_icon": "fas fa-list",
                     "description": "A list of comma separated antibodies to discard",
                     "type": "string",
                     "pattern": "(\\S+)?(,\\S+)*"
@@ -181,6 +182,7 @@
         },
         "graph_options": {
             "title": "Options for pixelator graph command.",
+            "type": "object",
             "properties": {
                 "multiplet_recovery": {
                     "description": "Activate the multiplet recovery using leiden community detection",
@@ -209,6 +211,7 @@
         },
         "annotate_options": {
             "title": "Options for pixelator annotate command.",
+            "type": "object",
             "properties": {
                 "min_size": {
                     "description": "The minimum size (pixels) a component/cell can have (disabled by default)",
@@ -233,11 +236,11 @@
         },
         "analysis_options": {
             "title": "Options for pixelator analysis command.",
+            "type": "object",
             "properties": {
                 "skip_analysis": {
                     "description": "Skip analysis step",
-                    "type": "boolean",
-                    "default": false
+                    "type": "boolean"
                 },
                 "compute_polarization": {
                     "description": "Compute polarization scores matrix (clusters by markers)",
@@ -251,8 +254,7 @@
                 },
                 "use_full_bipartite": {
                     "description": "Use the bipartite graph instead of the one-node projection when computing polarization, coabundance and colocalization scores",
-                    "type": "boolean",
-                    "default": false
+                    "type": "boolean"
                 },
                 "polarization_normalization": {
                     "description": "Which approach to use to normalize the antibody counts.",
@@ -264,8 +266,7 @@
                 "polarization_binarization": {
                     "fa_icon": "fas binary",
                     "description": "Transform the antibody counts to 0-1 (binarize) when computing polarization",
-                    "type": "boolean",
-                    "default": false
+                    "type": "boolean"
                 },
                 "colocalization_transformation": {
                     "type": "string",
@@ -295,11 +296,11 @@
         },
         "report_options": {
             "title": "Options for pixelator report command.",
+            "type": "object",
             "properties": {
                 "skip_report": {
                     "description": "Skip report generation",
-                    "type": "boolean",
-                    "default": false
+                    "type": "boolean"
                 }
             }
         },
@@ -310,7 +311,6 @@
             "properties": {
                 "pixelator_container": {
                     "type": "string",
-                    "format": "url",
                     "description": "Override the container image reference to use for all steps using the `pixelator` command.",
                     "help_text": "Use this to force the pipeline to use a different image version in all steps that use the pixelator command.\nThe pipeline is not garanteed to work when using different pixelator versions."
                 }