From 07eff4346f3ccf0990dd785f95a02059d18a3b64 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Wed, 8 Jun 2022 11:46:45 +0200
Subject: [PATCH] fix path to symbolic links

---
 modules/tiddit/sv/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/tiddit/sv/main.nf b/modules/tiddit/sv/main.nf
index ec4affe3..275ceb3f 100644
--- a/modules/tiddit/sv/main.nf
+++ b/modules/tiddit/sv/main.nf
@@ -24,7 +24,7 @@ process TIDDIT_SV {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    [[ -d $bwa_index ]] && for i in $bwa_index/*; do [[ -f $fasta && ! "\$i" =~ .*"$fasta".* ]] && ln -s $bwa_index/\$i ${fasta}.\${i##*.} || ln -s $bwa_index/\$i \$i; done
+    [[ -d $bwa_index ]] && for i in $bwa_index/*; do [[ -f $fasta && ! "\$i" =~ .*"$fasta".* ]] && ln -s \$i ${fasta}.\${i##*.} || ln -s \$i .; done
 
     tiddit \\
         --sv \\