From 85765b1b1ab75fea09c8d98ddec610d23879c064 Mon Sep 17 00:00:00 2001
From: Stephen Watts <hello@stephen.ac>
Date: Mon, 3 Jun 2024 18:39:24 +1000
Subject: [PATCH] Quote absolute paths used in directory shadowing

---
 modules/local/svprep/assemble/main.nf | 2 +-
 modules/local/svprep/call/main.nf     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/svprep/assemble/main.nf b/modules/local/svprep/assemble/main.nf
index d205b09f..08bdb91e 100644
--- a/modules/local/svprep/assemble/main.nf
+++ b/modules/local/svprep/assemble/main.nf
@@ -58,7 +58,7 @@ process GRIDSS_ASSEMBLE {
             # NOTE(SW): ideally we would get the relative path using the --relative-to but this is only
             # supported for GNU realpath and fails for others such as BusyBox, which is used in Biocontainers
             symlinkpath=\$(realpath \${filepath_src})
-            ln -s \${symlinkpath} \${filepath_dst};
+            ln -s "\${symlinkpath}" \${filepath_dst};
         done
         if [[ -L "\${src##*/}" ]]; then
             rm "\${src}"
diff --git a/modules/local/svprep/call/main.nf b/modules/local/svprep/call/main.nf
index ef28f83a..3cbb62c4 100644
--- a/modules/local/svprep/call/main.nf
+++ b/modules/local/svprep/call/main.nf
@@ -58,7 +58,7 @@ process GRIDSS_CALL {
             # NOTE(SW): ideally we would get the relative path using the --relative-to but this is only
             # supported for GNU realpath and fails for others such as BusyBox, which is used in Biocontainers
             symlinkpath=\$(realpath \${filepath_src})
-            ln -s \${symlinkpath} \${filepath_dst};
+            ln -s "\${symlinkpath}" \${filepath_dst};
         done
         if [[ -L "\${src##*/}" ]]; then
             rm "\${src}"