Upload data even when pipeline fails.

CLIP/iCLIP.snakefile

@@ -623,9 +623,12 @@ bam2bigwig.sh: bedGraphToBigWig failed
 
 
 onsuccess:
-    print("iCLIP data pre-processing finished.")
+    print("iCLIP data analysis finished.")
     cleanup_and_backup(output_dir, config)
 
 onerror:
-    print("iCLIP data pre-processing failed.")
+    shell(f"rm -rf {output_dir}_err")
+    shell(f"cp -rp {output_dir} {output_dir}_err")
+    cleanup_and_backup(output_dir + "_err", config)
+    print("iCLIP data analysis failed.")
 

PRO-seq/PRO-seq.snakefile

@@ -1537,5 +1537,8 @@ onsuccess:
     cleanup_and_backup(output_dir, config)
 
 onerror:
+    shell(f"rm -rf {output_dir}_err")
+    shell(f"cp -rp {output_dir} {output_dir}_err")
+    cleanup_and_backup(output_dir + "_err", config)
     print("PRO-seq analysis failed.")
 

small_RNA-seq/small_RNA-seq.snakefile

@@ -3865,20 +3865,11 @@ def try_to_cluster_genes(counts_data):
 onsuccess:
     print("small RNA-seq analysis finished.")
     cleanup_and_backup(output_dir, config)
-    # print("removing metadata")
-    # # https://stackoverflow.com/a/45614282/1878788
-    # rmtree(".snakemake/metadata")
-    # if config.get("backup", {}):
-    #     user = config["backup"]["user"]
-    #     if user == "USER":
-    #         user = os.environ[user]
-    #     host = config["backup"]["host"]
-    #     # If no dest_dir, we assume the directory structure
-    #     # is the same on the destination host
-    #     dest_dir = config["backup"].get("dest_dir", os.getcwd())
-    #     print(f"backuping results to {user}@{host}:{dest_dir}")
-    #     shell(f"rsync -vaP {output_dir} {user}@{host}:{dest_dir}")
+
 
 onerror:
+    shell(f"rm -rf {output_dir}_err")
+    shell(f"cp -rp {output_dir} {output_dir}_err")
+    cleanup_and_backup(output_dir + "_err", config)
     print("small RNA-seq analysis failed.")