From b2bf20a4953cd6610007a12f9e4667e694e8aca0 Mon Sep 17 00:00:00 2001
From: Nicolas Servant <nicolas.servant@curie.fr>
Date: Fri, 21 May 2021 13:13:17 +0200
Subject: [PATCH] Update main.nf
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Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 4eb670d..6dfd2f6 100644
--- a/main.nf
+++ b/main.nf
@@ -697,7 +697,7 @@ process remove_duplicates {
    mkdir -p stats/${sample}
 
    ## Sort valid pairs and remove read pairs with same starts (i.e duplicated read pairs)
-   sort -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m ${vpairs} | \
+   sort -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m ${vpairs} | \\
    awk -F"\\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=\$2 || c2!=\$5 || s1!=\$3 || s2!=\$6){print;c1=\$2;c2=\$5;s1=\$3;s2=\$6}' > ${sample}.allValidPairs
 
    echo -n "valid_interaction\t" > ${sample}_allValidPairs.mergestat
-- 
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