From df0bbc29e1a13d765c49d92d4fe116b66171783a Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 11 Apr 2018 13:50:08 +0200
Subject: [PATCH] Upload data even when pipeline fails.
---
CLIP/iCLIP.snakefile | 7 +++++--
PRO-seq/PRO-seq.snakefile | 3 +++
small_RNA-seq/small_RNA-seq.snakefile | 17 ++++-------------
3 files changed, 12 insertions(+), 15 deletions(-)
diff --git a/CLIP/iCLIP.snakefile b/CLIP/iCLIP.snakefile
index 9e9dfec..dcde8f8 100644
--- a/CLIP/iCLIP.snakefile
+++ b/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.")
diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile
index b2b24fe..12b1075 100644
--- a/PRO-seq/PRO-seq.snakefile
+++ b/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.")
diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile
index 43b6dd7..81041c2 100644
--- a/small_RNA-seq/small_RNA-seq.snakefile
+++ b/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.")
--
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