From e8d599075f84f4235377cc1c2621facf05d88716 Mon Sep 17 00:00:00 2001
From: Emma Rousseau <emmarou1@icloud.com>
Date: Sun, 6 Oct 2024 13:30:26 +0200
Subject: [PATCH] fix buf with mv command

---
 src/snpeff/config.vsh.yaml | 3 +--
 src/snpeff/script.sh       | 8 ++++----
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/src/snpeff/config.vsh.yaml b/src/snpeff/config.vsh.yaml
index 13492392..1ad361e3 100644
--- a/src/snpeff/config.vsh.yaml
+++ b/src/snpeff/config.vsh.yaml
@@ -283,8 +283,7 @@ resources:
 test_resources:
   - type: bash_script
     path: test.sh
-  - type: file
-    path: test_data
+  - path: test_data
 engines:
   - type: docker
     image: quay.io/staphb/snpeff:5.2a
diff --git a/src/snpeff/script.sh b/src/snpeff/script.sh
index 975c8eb9..d547c486 100644
--- a/src/snpeff/script.sh
+++ b/src/snpeff/script.sh
@@ -138,17 +138,17 @@ directory_path=$(dirname "$absolute_path")
 # Move the automatically generated outputs to their locations
 if [ -z "$par_no_stats" ]; then
     if [ ! -z "$par_summary" ]; then
-    mv -f snpEff_summary.html "$par_summary"
+    mv -fn snpEff_summary.html "$par_summary"
     else
-    mv -f snpEff_summary.html "$directory_path"
+    mv -fn snpEff_summary.html "$directory_path"
     fi
 fi
 
 if [ -z "$par_no_stats" ]; then
     if [ ! -z "$par_genes" ]; then
-    mv -f snpEff_genes.txt "$par_genes"
+    mv -fn snpEff_genes.txt "$par_genes"
     else
-    mv -f snpEff_genes.txt "$directory_path"
+    mv -fn snpEff_genes.txt "$directory_path"
     fi
 fi