diff --git a/nextflow.config b/nextflow.config
index f7ebe5c..add4067 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -206,11 +206,13 @@ params {
     xorf_custom_database                    = null    // custom protein db: .dmnd/.dmnd.gz replaces default; .fa/.fasta/.fa.gz appended to SwissProt and reindexed
     xorf_chunk_size                         = 20      // chunk size for XORF parallel processing
     xorf_skip_netstart                      = true    // skip netstart
-    xorf_predict_min_score_max_predictions  = 0.50    // min score for ORF predictions
+    xorf_skip_transaid                      = false   // skip TransAID; PREDICT scores with its no-TransAID model
+    xorf_predict_min_score_max_predictions  = -1      // negative: model bundle cutoff (0.29; 0.33 with skip_transaid)
     xorf_predict_max_predictions            = 3       // max ORF predictions per region
-    xorf_predict_threshold                  = 0.03    // prediction threshold
+    xorf_predict_threshold                  = -1      // negative: model bundle cutoff; only sets predicted_class
     xorf_predict_keep_raw                   = false   // keep raw predictions
     xorf_do_polishing                       = true    // polish ORFs (duplicates, truncations)
+    xorf_strip_truncations                  = true    // drop predictions flagged as 5' truncations
     xorf_skip_joined_concat                 = false   // skip joined concatenation of chunks
     xorf_rename_deactivate                  = false   // disable ORF renaming
     xorf_rename_rebase                      = false   // rebase names to short hashes
@@ -940,6 +942,11 @@ process {
               base_args = base_args + ' --keep-raw'
             }
 
+            // Without TransAID scores, score with the bundled model trained without them.
+            if (params.xorf_skip_transaid) {
+              base_args = base_args + ' --no-transaid'
+            }
+
             if (base_args.size() > 0) {
               return base_args.join(' ')
             } else {
diff --git a/params.json b/params.json
index af10c23..d26bdbd 100644
--- a/params.json
+++ b/params.json
@@ -88,11 +88,13 @@
     "xorf_custom_database":                   null,
     "xorf_chunk_size":                        20,
     "xorf_skip_netstart":                     true,
-    "xorf_predict_min_score_max_predictions": 0.50,
+    "xorf_skip_transaid":                     false,
+    "xorf_predict_min_score_max_predictions": -1,
     "xorf_predict_max_predictions":           3,
-    "xorf_predict_threshold":                 0.03,
+    "xorf_predict_threshold":                 -1,
     "xorf_predict_keep_raw":                  false,
     "xorf_do_polishing":                      true,
+    "xorf_strip_truncations":                 true,
     "xorf_skip_joined_concat":                false,
     "xorf_rename_deactivate":                 false,
     "xorf_rename_rebase":                     true,
diff --git a/subworkflows/xorf/main.nf b/subworkflows/xorf/main.nf
index f1a4d25..4dd4bcc 100644
--- a/subworkflows/xorf/main.nf
+++ b/subworkflows/xorf/main.nf
@@ -169,9 +169,14 @@ workflow XORF_RUN {
             ch_esm_weights,
             params.xorf_predict_keep_raw,
             params.xorf_selenocysteine_sites,                          
+            // Keep this positional order in sync with modules/xorf/src/subworkflows/xorf/main.nf.
+            // v0.1.2 added skip_transaid after skip_netstart and strip_truncations after
+            // do_polishing; v0.2.0 keeps the same 19-input signature.
             params.xorf_skip_netstart,
+            params.xorf_skip_transaid,
             params.xorf_rename_deactivate,
             params.xorf_do_polishing,
+            params.xorf_strip_truncations,
             params.xorf_skip_joined_concat,
             false, null, null,             // run_only_on / run_only_mode / run_only_target — masking not ported
             ch_database_versions.mix(ch_esm_versions)