modified: bcbio.array.pbs

modified: cre.sh
naumenko-sa · Oct 17, 2018 · 2838f81 · 2838f81
1 parent 1d92514
commit 2838f81
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Showing 2 changed files with 3 additions and 8 deletions.
diff --git 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
@@ -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