From 68aac6f304e10b362d93965fb9b3f3e5e13818a1 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Sun, 30 Aug 2020 16:57:13 -0500
Subject: [PATCH] update biohpc var
---
variants/germline_vc.sh | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index 59c5d05..a4ff47e 100755
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -83,12 +83,15 @@ then
bgzip ${pair_id}.sam.vcf
elif [[ $algo == 'fb' ]]
then
+ paropt="--delay 1 --jobs 0 --memfree 2G"
if [[ -z $isdocker ]]
then
module load freebayes/gcc/1.2.0 parallel/20150122
paropt="--delay 2 -j $NPROC"
- else
- paropt="--delay 1 --jobs 0 --memfree 2G"
+ fi
+ if [[ -n $biohpc ]]
+ then
+ paropt="--delay 2 -j $NPROC"
fi
bamlist=''
for i in *.bam; do
--
GitLab