From 2838f81824c0e06dc88d20acce47179cde958824 Mon Sep 17 00:00:00 2001
From: naumenko-sa <evolgenomicslab@gmail.com>
Date: Wed, 17 Oct 2018 15:11:56 -0400
Subject: [PATCH] 	modified:   bcbio.array.pbs 	modified:   cre.sh

---
 bcbio.array.pbs | 2 +-
 cre.sh          | 9 ++-------
 2 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/bcbio.array.pbs b/bcbio.array.pbs
index f40f630..8b9cfa0 100644
--- a/bcbio.array.pbs
+++ b/bcbio.array.pbs
@@ -2,7 +2,7 @@
 #  runs bcbio for an array of projects listed in projects.txt
 #  run with qsub -t 1-500%100 bcbio.array.pbs
 #  check jobs with qstat -nt1 | grep naum
-#  100 is maximum reasonable amount of running jobs in the array
+#  100 is maximum reasonable amount of running jobs in the array, cluster has 316 nodes in total
 
 #PBS -l walltime=240:00:00,nodes=1:ppn=5
 #PBS -joe .
diff --git a/cre.sh b/cre.sh
index fb25425..6c8222e 100755
--- a/cre.sh
+++ b/cre.sh
@@ -252,19 +252,14 @@ then
     f_cleanup
 fi
 
-#make report by default
-if [ -z $make_report ]
-then
-    make_report=1
-fi 
-
 if [ -z $max_af ]
 then
     max_af=0.01
 fi
 export max_af
 
-if [ $make_report -eq 1 ]
+#make report by default
+if [ -z $make_report ]  || [ $make_report -eq 1 ]
 then
     f_make_report
 fi