From f6ea096fa6e4a439d32bd934d4ad571eef0c5b40 Mon Sep 17 00:00:00 2001
From: Rachel  LEGENDRE <rachel.legendre@pasteur.fr>
Date: Wed, 10 Nov 2021 11:17:46 +0100
Subject: [PATCH] Update alienTrimmer.rules

---
 workflow/rules/alienTrimmer.rules | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/rules/alienTrimmer.rules b/workflow/rules/alienTrimmer.rules
index 54004be..5be5250 100755
--- a/workflow/rules/alienTrimmer.rules
+++ b/workflow/rules/alienTrimmer.rules
@@ -59,7 +59,7 @@ rule alienTrimmer:
         # paired end or single end
         if [[ ${{#infiles[@]}} -eq 2 ]];
         then
-            cmd+="-1 ${{infiles[0]}} -2 ${{infiles[1]}} -o out_paired"
+            cmd+=" -1 ${{infiles[0]}} -2 ${{infiles[1]}} -o out_paired"
         else
             cmd+=" -i ${{infiles[0]}} -o out_single"
         fi
-- 
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