From a47fe6ff199849385d34839d4b2d8cad91280361 Mon Sep 17 00:00:00 2001
From: JWesseling <161333482+JWesseling@users.noreply.github.com>
Date: Wed, 17 Apr 2024 08:55:27 +0200
Subject: [PATCH] Update makeblastdb.sh

Changed line 14,15 and 16 to be POSIX compliant
---
 workflow/scripts/makeblastdb.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/workflow/scripts/makeblastdb.sh b/workflow/scripts/makeblastdb.sh
index 1dd5354..4a69645 100644
--- a/workflow/scripts/makeblastdb.sh
+++ b/workflow/scripts/makeblastdb.sh
@@ -11,10 +11,10 @@ for i in $(seq 1 $ITERATIONS); do
 
   # only keep records with ott IDs, reformat the headers to retain the process ID, write to $TMP
   # start new file on first iteration, then append
-  if [[ ${i} == 1 ]]; then
-    egrep -A 1 'ott\d+' ${INFILE} | awk -F'|' '/^>/ {print ">"$3; next} {print}' > ${TMP}
+  if [ "${i}" -eq 1 ]; then
+    egrep -A 1 'ott[0-9]+' ${INFILE} | awk -F'|' '/^>/ {print ">"$3; next} {print}' > ${TMP}
   else
-    egrep -A 1 'ott\d+' ${INFILE} | awk -F'|' '/^>/ {print ">"$3; next} {print}' >> ${TMP}
+    egrep -A 1 'ott[0-9]+' ${INFILE} | awk -F'|' '/^>/ {print ">"$3; next} {print}' >> ${TMP}
   fi
 
 done