Update src/busco/busco/script.sh

Co-authored-by: Robrecht Cannoodt <[email protected]>

src/busco/busco/script.sh

@@ -56,19 +56,24 @@ busco \
 
 
 
+out_dir=$(find "$tmp_dir/$prefix" -maxdepth 1 -name 'run_*')
+
 if [[ -n "$par_short_summary_json" ]]; then
-    find "$tmp_dir/$prefix" -maxdepth 1 -type d -name 'run_*' -exec cp {}/short_summary.json "$par_short_summary_json" \;
+    cp "$out_dir/short_summary.json" "$par_short_summary_json"
 fi
 if [[ -n "$par_short_summary_txt" ]]; then
-    find "$tmp_dir/$prefix" -maxdepth 1 -type d -name 'run_*' -exec cp {}/short_summary.txt "$par_short_summary_txt" \;
+    cp "$out_dir/short_summary.txt" "$par_short_summary_txt"
 fi
 if [[ -n "$par_full_table" ]]; then
-    find "$tmp_dir/$prefix" -maxdepth 1 -type d -name 'run_*' -exec cp {}/full_table.tsv "$par_full_table" \;
+    cp "$out_dir/full_table.tsv" "$par_full_table"
 fi
 if [[ -n "$par_missing_busco_list" ]]; then
-    find "$tmp_dir/$prefix" -maxdepth 1 -type d -name 'run_*' -exec cp {}/missing_busco_list.tsv "$par_missing_busco_list" \;
+    cp "$out_dir/missing_busco_list.tsv" "$par_missing_busco_list"
 fi
 if [[ -n "$par_output_dir" ]]; then
-    cp -r $tmp_dir/$prefix/run_* $par_output_dir
+    if [[ -d "$par_output_dir" ]]; then
+        rm -r "$par_output_dir"
+    fi
+    cp -r "$out_dir" "$par_output_dir"
 fi