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