From 0bf3f2a523ccee1b05af61f1af9e99ab338c9cc0 Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Thu, 11 Jan 2018 09:42:44 +0100
Subject: [PATCH] Fix pipefail error when merging StrandphaseR output
---
Snakefile | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/Snakefile b/Snakefile
index 4b8811b..5333337 100644
--- a/Snakefile
+++ b/Snakefile
@@ -324,8 +324,9 @@ rule combine_strandphaser_output:
"strand_states/" + config["sample"] + ".strandphaser_output.txt"
shell:
"""
- cat {input} | head -n1 > {output}
- for x in {input}; do tail -n+2 $x >> {output}; done
+ set +o pipefail
+ cat {input} | head -n1 > {output};
+ for x in {input}; do tail -n+2 $x >> {output}; done;
"""
--
GitLab