From c4c0f64ae0c9d6cb5348e034c7901a228ee206d3 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 6 May 2021 09:25:44 +0200
Subject: [PATCH] flexi_splitter: double escape sed cmd

---
 src/nf_modules/flexi_splitter/main.nf | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/nf_modules/flexi_splitter/main.nf b/src/nf_modules/flexi_splitter/main.nf
index 47e67604..d846274a 100644
--- a/src/nf_modules/flexi_splitter/main.nf
+++ b/src/nf_modules/flexi_splitter/main.nf
@@ -49,9 +49,8 @@ process split_file {
   rm -Rf split/unassigned
   mkdir -p results/
   find split -type "f" | \
-    sed -E "s|(.*/split/(.*)/(.*))|\1 \2_\3|g" |
+    sed -E "s|(.*/split/(.*)/(.*))|\\1 \\2_\\3|g" |
     awk '{system("mv "\$1" results/"\$2)}'
-  rm -Rf split
   """
   else
   """
@@ -61,6 +60,5 @@ process split_file {
   find split -type "f" | \
     sed -E "s|(.*/split/(.*)/(.*))|\1 \2_\3|g" |
     awk '{system("mv "\$1" results/"\$2)}'
-  rm -Rf split
   """
 }
-- 
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