From 3e26851ab2be24b97e282d7cc976b37da9bb8764 Mon Sep 17 00:00:00 2001
From: E B Benson <117281795+Deriverx2@users.noreply.github.com>
Date: Fri, 17 Jul 2026 11:06:56 +0900
Subject: [PATCH 1/2] Fix symbolic link creation for fasta file

https://github.com/nf-core/methylseq/issues/608
---
 modules/nf-core/bwameth/align/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf
index 8177c12b4456..85e87fbf7c18 100644
--- a/modules/nf-core/bwameth/align/main.nf
+++ b/modules/nf-core/bwameth/align/main.nf
@@ -26,7 +26,7 @@ process BWAMETH_ALIGN {
     def prefix     = task.ext.prefix ?: "${meta.id}"
     """
     export BWA_METH_SKIP_TIME_CHECKS=1
-    ln -sf \$(readlink ${fasta}) ${index}/${fasta}
+    [ -e "${index}/${fasta}" ] || ln -s "$(readlink "${fasta}")" "${index}/${fasta}"
 
     bwameth.py \\
         ${args} \\

From b6e7d8c5d4b8f071d6762035b12e5a4373680669 Mon Sep 17 00:00:00 2001
From: E B Benson <117281795+Deriverx2@users.noreply.github.com>
Date: Fri, 17 Jul 2026 16:09:09 +0900
Subject: [PATCH 2/2] Fix syntax for symbolic link creation in main.nf for
 groovy parsing

---
 modules/nf-core/bwameth/align/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf
index 85e87fbf7c18..08beb15245cb 100644
--- a/modules/nf-core/bwameth/align/main.nf
+++ b/modules/nf-core/bwameth/align/main.nf
@@ -26,7 +26,7 @@ process BWAMETH_ALIGN {
     def prefix     = task.ext.prefix ?: "${meta.id}"
     """
     export BWA_METH_SKIP_TIME_CHECKS=1
-    [ -e "${index}/${fasta}" ] || ln -s "$(readlink "${fasta}")" "${index}/${fasta}"
+    [ -e "${index}/${fasta}" ] || ln -s \$(readlink ${fasta}) ${index}/${fasta}
 
     bwameth.py \\
         ${args} \\