From c14c5d2acbc0b56fb27d28bac80ad282554f8293 Mon Sep 17 00:00:00 2001
From: MarieLataretu <marie.lataretu@uni-jena.de>
Date: Fri, 18 Feb 2022 18:10:20 +0100
Subject: [PATCH] Index fails when FASTAs have different line len Fixes #52

---
 modules/get_host.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/get_host.nf b/modules/get_host.nf
index 498aeef..b9d47be 100644
--- a/modules/get_host.nf
+++ b/modules/get_host.nf
@@ -56,11 +56,12 @@ process check_own {
   """
   # -L for following a symbolic link
   if ! ( file -L $fasta | grep -q 'gzip compressed' ); then
+    sed -i -e '\$a\\' ${fasta}
     bgzip -@ ${task.cpus} < ${fasta} > ${fasta}.gz
     # now $fasta'.gz'
   else
     mv ${fasta} ${fasta}.tmp
-    zcat ${fasta}.tmp | bgzip -@ ${task.cpus} -c > ${fasta}.gz
+    zcat ${fasta}.tmp | sed -e '\$a\\' | bgzip -@ ${task.cpus} -c > ${fasta}.gz
   fi
   """
 }