Quote absolute paths used in directory shadowing

nf-core · Jun 4, 2024 · 85765b1 · 85765b1
1 parent 9abc114
commit 85765b1
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git 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
@@ -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}"