diff --git a/modules/local/diann/assemble_empirical_library/main.nf b/modules/local/diann/assemble_empirical_library/main.nf
index c0c069e..c2d8a5a 100644
--- a/modules/local/diann/assemble_empirical_library/main.nf
+++ b/modules/local/diann/assemble_empirical_library/main.nf
@@ -49,6 +49,9 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
     diann_im_window = params.im_window ? "--im-window $params.im_window" : ""
     diann_dda_flag = meta.acquisition_method == 'dda' ? "--dda" : ""
 
+    diann_channel_run_norm = params.channel_run_norm ? "--channel-run-norm" : ""
+    diann_channel_spec_norm = params.channel_spec_norm ? "--channel-spec-norm" : ""
+
     """
     # Precursor Tolerance value was: ${meta['precursormasstolerance']}
     # Fragment Tolerance value was: ${meta['fragmentmasstolerance']}
@@ -76,6 +79,8 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
             ${diann_tims_sum} \\
             ${diann_im_window} \\
             ${diann_dda_flag} \\
+            ${diann_channel_run_norm} \\
+            ${diann_channel_spec_norm} \\
             \${mod_flags} \\
             $args \\
             2>&1 | tee assemble_empirical_library.log
diff --git a/modules/local/diann/individual_analysis/main.nf b/modules/local/diann/individual_analysis/main.nf
index db23607..9273a4c 100644
--- a/modules/local/diann/individual_analysis/main.nf
+++ b/modules/local/diann/individual_analysis/main.nf
@@ -88,6 +88,9 @@ process INDIVIDUAL_ANALYSIS {
     min_fr_mz = meta['ms2minmz'] ? "--min-fr-mz ${meta['ms2minmz']}" : ""
     max_fr_mz = meta['ms2maxmz'] ? "--max-fr-mz ${meta['ms2maxmz']}" : ""
 
+    diann_channel_run_norm = params.channel_run_norm ? "--channel-run-norm" : ""
+    diann_channel_spec_norm = params.channel_spec_norm ? "--channel-spec-norm" : ""
+
     """
     # Extract --var-mod, --fixed-mod, and --monitor-mod flags from diann_config.cfg
     mod_flags=\$(grep -oP '(--var-mod\\s+\\S+|--fixed-mod\\s+\\S+|--monitor-mod\\s+\\S+|--lib-fixed-mod\\s+\\S+|--original-mods|--channels\\s+.+)' ${diann_config} | tr '\\n' ' ')
@@ -114,6 +117,8 @@ process INDIVIDUAL_ANALYSIS {
             ${diann_tims_sum} \\
             ${diann_im_window} \\
             ${diann_dda_flag} \\
+            ${diann_channel_run_norm} \\
+            ${diann_channel_spec_norm} \\
             \${mod_flags} \\
             $args \\
             2>&1 | tee ${ms_file.baseName}_final_diann.log
diff --git a/modules/local/diann/preliminary_analysis/main.nf b/modules/local/diann/preliminary_analysis/main.nf
index 6c6b91d..79a7dc1 100644
--- a/modules/local/diann/preliminary_analysis/main.nf
+++ b/modules/local/diann/preliminary_analysis/main.nf
@@ -69,6 +69,9 @@ process PRELIMINARY_ANALYSIS {
     min_fr_mz = meta['ms2minmz'] ? "--min-fr-mz ${meta['ms2minmz']}" : ""
     max_fr_mz = meta['ms2maxmz'] ? "--max-fr-mz ${meta['ms2maxmz']}" : ""
 
+    diann_channel_run_norm = params.channel_run_norm ? "--channel-run-norm" : ""
+    diann_channel_spec_norm = params.channel_spec_norm ? "--channel-spec-norm" : ""
+
     """
     # Precursor Tolerance value was: ${meta['precursormasstolerance']}
     # Fragment Tolerance value was: ${meta['fragmentmasstolerance']}
@@ -99,6 +102,8 @@ process PRELIMINARY_ANALYSIS {
             ${diann_im_window} \\
             --no-prot-inf \\
             ${diann_dda_flag} \\
+            ${diann_channel_run_norm} \\
+            ${diann_channel_spec_norm} \\
             \${mod_flags} \\
             $args \\
             2>&1 | tee ${ms_file.baseName}_diann.log