diff --git a/conf/modules.config b/conf/modules.config
index 25de8b9..6bd573f 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -374,6 +374,11 @@ process {
     }
     withName: '.*:LONGPHASE_HAPLOTAG*' {
         ext.prefix = { "${meta.id}_${meta.type}" }
+        ext.args   = {
+                [
+                    params.longphase_tag_supplementary ? "--tagSupplementary" : ''
+                ].join(' ').trim()
+            }
         publishDir = [
             path: { "${params.outdir}/${meta.id}/bamfiles" },
             mode: params.publish_dir_mode,
diff --git a/docs/usage.md b/docs/usage.md
index a644732..e7944b3 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -152,6 +152,12 @@ If you want to run with a CHM13 reference without using `--genome CHM13` (for ex
 | `--skip_modkit`        | A boolean to skip the modkit pileup step. Default = `false`                                                                                                                          |
 | `--skip_whatshapstats` | A boolean to skip WhatsHap phasing statistics. Default = `false`                                                                                                                     |
 
+#### LONGPHASE options:
+
+| Parameter                       | Description                                                                        |
+| ------------------------------- | ---------------------------------------------------------------------------------- |
+| `--longphase_tag_supplementary` | Include supplementary alignments in Longphase haplotype tagging. Default = `false` |
+
 #### VEP options:
 
 | Parameter              | Description                                                                                                                                      |
@@ -200,7 +206,7 @@ If you want to run with a CHM13 reference without using `--genome CHM13` (for ex
 
 | Parameter              | Description                                                                          |
 | ---------------------- | ------------------------------------------------------------------------------------ |
-| `--severus_minsupport` | Minimum number of supporting reads required for SEVERUS to call an SV. Default = `5` |
+| `--severus_minsupport` | Minimum number of supporting reads required for SEVERUS to call an SV. Default = `3` |
 
 #### WAKHAN Options
 
diff --git a/nextflow.config b/nextflow.config
index 84c9f48..c0dbb53 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -22,6 +22,9 @@ params {
     prioritize_caller_somatic   = 'deepsomatic'
     generate_gvcf               = false
 
+    // Longphase options
+    longphase_tag_supplementary = false
+
     // PON Options
     clairsto_pon_vcfs           = null
     clairsto_pon_flags          = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index a7cc149..ae16d4c 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -68,22 +68,24 @@
             "type": "object",
             "properties": {
                 "germline_var_keep": {
-                    "type": "array",
+                    "type": ["string", "array"],
                     "description": "List of germline variant callers to use. Must include at least one of [deepvariant, clair].",
                     "items": {
                         "type": "string",
                         "enum": ["deepvariant", "clair"]
                     },
-                    "minItems": 1
+                    "minItems": 1,
+                    "default": "['deepvariant', 'clair']"
                 },
                 "somatic_var_keep": {
-                    "type": "array",
+                    "type": ["string", "array"],
                     "description": "List of somatic variant callers to use. Must include at least one of [deepsomatic, clair].",
                     "items": {
                         "type": "string",
                         "enum": ["deepsomatic", "clair"]
                     },
-                    "minItems": 1
+                    "minItems": 1,
+                    "default": "['deepsomatic', 'clair']"
                 },
                 "germline_var_combine": {
                     "type": "string",
@@ -111,6 +113,18 @@
                 }
             }
         },
+        "longphase_options": {
+            "title": "Longphase options",
+            "type": "object",
+            "description": "Options for Longphase phasing of small variants",
+            "properties": {
+                "longphase_tag_supplementary": {
+                    "type": "boolean",
+                    "description": "Whether to include supplementary alignments in Longphase haplotype tagging.",
+                    "default": false
+                }
+            }
+        },
         "reference_genome_options": {
             "title": "Reference genome options",
             "type": "object",
@@ -126,7 +140,6 @@
                 },
                 "igenomes_ignore": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Do not load the iGenomes reference config.",
                     "fa_icon": "fas fa-ban",
                     "hidden": true,
@@ -202,7 +215,6 @@
                 },
                 "download_vep_cache": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Download the VEP cache if not already present"
                 },
                 "vep_custom": {
@@ -283,7 +295,6 @@
                 },
                 "ascat_pdf_plots": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Boolean for ASCAT production of pdf plots (entered as string)"
                 }
             }
@@ -307,72 +318,58 @@
             "properties": {
                 "skip_qc": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skips all QC steps"
                 },
                 "skip_cramino": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skips Cramino"
                 },
                 "skip_mosdepth": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skips Mosdepth"
                 },
                 "skip_bamstats": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skips samtools flagstat, stats, and idxstats"
                 },
                 "skip_wakhan": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skips wakhan"
                 },
                 "skip_fiber": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skip Fibertools steps"
                 },
                 "skip_ascat": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skip ASCAT"
                 },
                 "skip_m6a": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skip m6a calling by Fibertools"
                 },
                 "skip_vep": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skip VEP annotation"
                 },
                 "skip_normalfiber": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skip Fibertools steps for the normal sample"
                 },
                 "skip_nanoplot": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skip Nanoplot"
                 },
                 "skip_whatshapstats": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skip WhatsHap stats"
                 },
                 "skip_modcall": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Skip modification calling"
                 },
                 "use_gpu": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Use GPU for supported tools (e.g. DeepVariant, DeepSomatic, Clair3)"
                 }
             }
@@ -434,7 +431,6 @@
             "properties": {
                 "version": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Display version and exit.",
                     "fa_icon": "fas fa-question-circle",
                     "hidden": true
@@ -458,7 +454,6 @@
                 },
                 "plaintext_email": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Send plain-text email instead of HTML.",
                     "fa_icon": "fas fa-remove-format",
                     "hidden": true
@@ -473,7 +468,6 @@
                 },
                 "monochrome_logs": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Do not use coloured log outputs.",
                     "fa_icon": "fas fa-palette",
                     "hidden": true
@@ -525,17 +519,14 @@
                 },
                 "help": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Display the help message."
                 },
                 "help_full": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Display the full detailed help message."
                 },
                 "show_hidden": {
                     "type": "boolean",
-                    "default": false,
                     "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)."
                 }
             }
@@ -551,6 +542,9 @@
         {
             "$ref": "#/$defs/small_variant_calling_options"
         },
+        {
+            "$ref": "#/$defs/longphase_options"
+        },
         {
             "$ref": "#/$defs/reference_genome_options"
         },
@@ -581,5 +575,13 @@
         {
             "$ref": "#/$defs/generic_options"
         }
-    ]
+    ],
+    "properties": {
+        "generate_gvcf": {
+            "type": "boolean"
+        },
+        "skip_modkit": {
+            "type": "boolean"
+        }
+    }
 }