From df4c8d91ca6d16c34c397fd1e0e6b2afbf6cf2cc Mon Sep 17 00:00:00 2001
From: Vladimir Mikryukov <v.mikryukov@gmail.com>
Date: Thu, 2 Mar 2023 11:18:52 +0200
Subject: [PATCH] =?UTF-8?q?bug=20fixed=20in=20`assemble=5Fits`=20(thanks?=
 =?UTF-8?q?=20to=20Kadri=20P=C3=B5ldmaa=20for=20discovering=20the=20error)?=
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---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index a1feb0b..5b0b3cd 100644
--- a/main.nf
+++ b/main.nf
@@ -1175,7 +1175,7 @@ process assemble_its {
       ## Convert table back to fasta
       ## Remove leading and trailing Ns
       echo -e "\n..Preparing fasta"
-      awk 'NR>1 { print \$1 "\t" \$2 }' tmp_2_ITS1_58S_ITS2.txt \
+      awk 'NR>1 { print \$1 "\t" \$2\$3\$4 }' tmp_2_ITS1_58S_ITS2.txt \
         | seqkit tab2fx -w 0  \
         | seqkit replace -p "^n+|n+\$" -r "" -is -w 0 \
         | gzip -6 > ${sampID}_ITS1_58S_ITS2.fasta.gz