fix buf with mv command

viash-hub · Oct 6, 2024 · e8d5990 · e8d5990
1 parent 1ed80fb
commit e8d5990
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 6 deletions.
diff --git 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
@@ -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