From ce224044ee13db9647b74a6cba726006f04ec861 Mon Sep 17 00:00:00 2001
From: silask <silas.kieser@gmail.com>
Date: Wed, 25 Oct 2023 16:09:12 +0200
Subject: [PATCH] fix #701

---
 workflow/rules/genecatalog.smk | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/workflow/rules/genecatalog.smk b/workflow/rules/genecatalog.smk
index f82e0a2a..4b2c7eb5 100644
--- a/workflow/rules/genecatalog.smk
+++ b/workflow/rules/genecatalog.smk
@@ -486,15 +486,24 @@ rule eggNOG_annotation:
         "logs/genecatalog/annotation/eggnog/{subset}_annotate_hits_table.log",
     shell:
         """
-
-        if [ {params.copyto_shm} == "t" ] ;
-        then
-            cp {EGGNOG_DIR}/eggnog.db {params.data_dir}/eggnog.db 2> {log}
-            cp {EGGNOG_DIR}/eggnog_proteins.dmnd {params.data_dir}/eggnog_proteins.dmnd 2>> {log}
+        if [ {params.copyto_shm} == "t" ] ; then
+            # Check if the files exist before copying
+            if [ ! -e "{params.data_dir}/eggnog.db" ]; then
+                cp {EGGNOG_DIR}/eggnog.db {params.data_dir}/eggnog.db 2> {log}
+            else
+                echo "File {params.data_dir}/eggnog.db already exists. Skipping copy." >> {log}
+            fi
+
+            if [ ! -e "{params.data_dir}/eggnog_proteins.dmnd" ]; then
+                cp {EGGNOG_DIR}/eggnog_proteins.dmnd {params.data_dir}/eggnog_proteins.dmnd 2>> {log}
+            else
+                echo "File {params.data_dir}/eggnog_proteins.dmnd already exists. Skipping copy." >> {log}
+            fi
         fi
 
         emapper.py --annotate_hits_table {input.seed} --no_file_comments \
           --override -o {params.prefix} --cpu {threads} --data_dir {params.data_dir} 2>> {log}
+
         """