From 73634a7da8431c60fddfcbc04d29af1d52b7a7e5 Mon Sep 17 00:00:00 2001
From: cyborgdnx <151539846+cyborgdnx@users.noreply.github.com>
Date: Wed, 29 Apr 2026 07:39:47 +0100
Subject: [PATCH 1/2] Rename parameter 'annotation' to 'annotation_type'

---
 modules/subworkflows/liftover.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/subworkflows/liftover.nf b/modules/subworkflows/liftover.nf
index 2853341..34bf85e 100644
--- a/modules/subworkflows/liftover.nf
+++ b/modules/subworkflows/liftover.nf
@@ -8,7 +8,7 @@ workflow LIFTOVER {
         ch_annot
         ch_tgt
     main:   
-        if (params.annotation != 'bed'){ 
+        if (params.annotation_type != 'bed'){ 
             log.info "Using CrossMap"
             lifted = crossmap(chain, ch_annot, ch_tgt)
         } else {
@@ -22,4 +22,4 @@ workflow LIFTOVER {
         features_stats( ch_annot, lifted.lifted_ch )
     emit:
         features_stats.out
-}
\ No newline at end of file
+}

From 3470dc028aed7561eb90bc0cf30c05a63d9806b7 Mon Sep 17 00:00:00 2001
From: cyborgdnx <151539846+cyborgdnx@users.noreply.github.com>
Date: Wed, 29 Apr 2026 07:41:54 +0100
Subject: [PATCH 2/2] Update liftover.nf

---
 modules/subworkflows/liftover.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/subworkflows/liftover.nf b/modules/subworkflows/liftover.nf
index 34bf85e..ffaea9f 100644
--- a/modules/subworkflows/liftover.nf
+++ b/modules/subworkflows/liftover.nf
@@ -8,7 +8,7 @@ workflow LIFTOVER {
         ch_annot
         ch_tgt
     main:   
-        if (params.annotation_type != 'bed'){ 
+        if (params.annotation_format != 'bed'){ 
             log.info "Using CrossMap"
             lifted = crossmap(chain, ch_annot, ch_tgt)
         } else {