From a2d0dca9f4be20e29337acc3dbf01700e7441126 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 21 May 2019 14:40:03 -0500
Subject: [PATCH] more nodes strelka
---
variants/germline_vc.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index d16aad9..c24e3c3 100755
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -124,8 +124,8 @@ then
gvcflist="$gvcflist --bam ${i}"
done
configManta.py $gvcflist --referenceFasta ${reffa} $mode --runDir manta
- manta/runWorkflow.py -m local -j 8
+ manta/runWorkflow.py -m local -j $SLURM_CPUS_ON_NODE
configureStrelkaGermlineWorkflow.py $gvcflist --referenceFasta ${reffa} $mode --indelCandidates manta/results/variants/candidateSmallIndels.vcf.gz --runDir strelka
- strelka/runWorkflow.py -m local -j 8
+ strelka/runWorkflow.py -m local -j $SLURM_CPUS_ON_NODE
bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.strelka2.vcf.gz strelka/results/variants/variants.vcf.gz
fi
--
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