diff --git a/main.nf b/main.nf
index 477f054..6fba958 100644
--- a/main.nf
+++ b/main.nf
@@ -195,7 +195,15 @@ workflow {
             params.extraexons
         )
 
-        ALIGN(blosumfile, PREPARE.out.alignment_input, PREPARE.out.clusters_split_ch)
+        ALIGN(
+            blosumfile,
+            PREPARE.out.alignment_input,
+            PREPARE.out.clusters_split_ch,
+            params.long_dist,
+            params.medium_dist,
+            params.short_dist,
+        )
+
         SCORE(ALIGN.out.folder_jscores, PREPARE.out.clusters_split_ch, PREPARE.out.dist_ranges_ch, params.bonafide_pairs)
         CLUSTER(SCORE.out.score_exon_hits_pairs, PREPARE.out.clusters_split_ch, clusterfile_ch, orthopairs_ch)
     }
diff --git a/modules/local/exorthist/align_pairs.nf b/modules/local/exorthist/align_pairs.nf
index afadeb5..007a2a4 100644
--- a/modules/local/exorthist/align_pairs.nf
+++ b/modules/local/exorthist/align_pairs.nf
@@ -5,6 +5,9 @@ process PARSE_IPA_PROT_ALN {
     input:
     path blosumfile
     tuple val(combid), path(sp1), path(sp2), path(cls_part_file), val(dist_range)
+    val long_dist
+    val medium_dist
+    val short_dist
 
     output:
     tuple val("${sp1.name}-${sp2.name}"), path("${sp1.name}-${sp2.name}-*"), emit: aligned_subclusters_4_splitting
@@ -17,13 +20,13 @@ process PARSE_IPA_PROT_ALN {
 
     switch(dist_range) {
         case "long":
-            dist_range_par = params.long_dist.split(",")
+            dist_range_par = long_dist.split(",")
             break
         case "medium":
-            dist_range_par = params.medium_dist.split(",")
+            dist_range_par = medium_dist.split(",")
             break
         case "short":
-            dist_range_par = params.short_dist.split(",")
+            dist_range_par = short_dist.split(",")
             break
     }
 
diff --git a/subworkflows/local/exorthist/align.nf b/subworkflows/local/exorthist/align.nf
index 7ad58fa..da1f067 100644
--- a/subworkflows/local/exorthist/align.nf
+++ b/subworkflows/local/exorthist/align.nf
@@ -11,11 +11,14 @@ workflow ALIGN {
     blosumfile
     alignment_input
     clusters_split_ch
+    long_dist
+    medium_dist
+    short_dist
 
     main:
     // the last argument is the protein similarity alignment.
     // if a prevaln folder is provided, the protein alignments present in each species pair subfolder will not be repeated.
-    PARSE_IPA_PROT_ALN(blosumfile, alignment_input)
+    PARSE_IPA_PROT_ALN(blosumfile, alignment_input, long_dist, medium_dist, short_dist)
 
     // Collapse EXs_to_split in batches of 500 files
     EXs_to_split = PARSE_IPA_PROT_ALN.out.EXs_to_split