diff --git a/modules/bigbio/onsite/main.nf b/modules/bigbio/onsite/main.nf
index ee6cff1..804d6eb 100644
--- a/modules/bigbio/onsite/main.nf
+++ b/modules/bigbio/onsite/main.nf
@@ -19,11 +19,12 @@ process ONSITE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.mzml_id}"
 
-    // Algorithm selection: ascore (default), phosphors, or lucxor
-    def algorithm = params.onsite_algorithm ?: 'ascore'
+    // Algorithm selection: lucxor (default), ascore, or phosphors
+    def algorithm = params.onsite_algorithm ?: 'lucxor'
 
     // Common parameters for all algorithms
     def fragment_tolerance = params.onsite_fragment_tolerance ?: '0.05'
+    def compute_all_scores = params.onsite_compute_all_scores ? '--compute-all-scores' : ''
 
     // Set default value for add_decoys (can be overridden by setting params.onsite_add_decoys = false)
     def onsite_add_decoys = params.containsKey('onsite_add_decoys') ? params.onsite_add_decoys : true
@@ -47,8 +48,8 @@ process ONSITE {
             --fragment-mass-tolerance ${fragment_tolerance} \\
             --fragment-mass-unit ${fragment_unit} \\
             ${add_decoys} \\
-            ${debug} \\
-            ${args}
+            ${compute_all_scores} \\
+            ${debug}
         """
     } else if (algorithm == 'phosphors') {
         // PhosphoRS: uses -in, -id, -out, --fragment-mass-unit
@@ -61,8 +62,8 @@ process ONSITE {
             --fragment-mass-tolerance ${fragment_tolerance} \\
             --fragment-mass-unit ${fragment_unit} \\
             ${add_decoys} \\
-            ${debug} \\
-            ${args}
+            ${compute_all_scores} \\
+            ${debug}
         """
     } else if (algorithm == 'lucxor') {
         // LucXor: uses -in, -id, -out, --fragment-error-units (note: error-units not mass-unit)
@@ -74,8 +75,10 @@ process ONSITE {
         def max_num_perm = params.onsite_max_num_perm ?: '16384'
         def modeling_threshold = params.onsite_modeling_score_threshold ?: '0.95'
         def scoring_threshold = params.onsite_scoring_threshold ?: '0.0'
-        def min_num_psms = params.onsite_min_num_psms_model ?: '50'
+        def min_num_psms = params.onsite_min_num_psms_model ?: '5'
         def rt_tolerance = params.onsite_rt_tolerance ?: '0.01'
+        def min_psms = params.onsite_min_psms ?: '5'
+        def disable_split_by_charge = params.onsite_disable_split_by_charge ? '--disable-split-by-charge' : ''
 
         // Optional target modifications - default for LucXor includes decoy
         def target_mods = params.onsite_target_modifications ? "--target-modifications ${params.onsite_target_modifications}" : "--target-modifications 'Phospho(S),Phospho(T),Phospho(Y),PhosphoDecoy(A)'"
@@ -103,8 +106,9 @@ process ONSITE {
             --scoring-threshold ${scoring_threshold} \\
             --min-num-psms-model ${min_num_psms} \\
             --rt-tolerance ${rt_tolerance} \\
-            ${debug} \\
-            ${args}
+            ${disable_split_by_charge} \\
+            ${compute_all_scores} \\
+            ${debug}
         """
     } else {
         error "Unknown onsite algorithm: ${algorithm}. Supported algorithms: ascore, phosphors, lucxor"
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index b9a5108..b60e54e 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -18,6 +18,12 @@ params {
                 // quantms results - using LFQ example as quantms results
                 quantms_results = "https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/LFQ_PXD007683.zip"
             }
+            onsite {
+                // Test data for onsite PTM localization module
+                // Using GitHub media links to download LFS files
+                mzml = "https://media.githubusercontent.com/media/weizhongchun/test-data/main/data/1.mzML"
+                idxml = "https://raw.githubusercontent.com/weizhongchun/test-data/main/data/1_consensus_fdr_filter_pep.idXML"
+            }
         }
     }
 }