From 18bc27a131588a1b433ce2a22f870a8541b8f0e3 Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryam7@users.noreply.github.com>
Date: Sun, 28 Jun 2020 17:53:55 -0700
Subject: [PATCH] allow strelka to run in local mode

---
 callers/illumina-strelka | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/callers/illumina-strelka b/callers/illumina-strelka
index 1f9eff6..638e068 100755
--- a/callers/illumina-strelka
+++ b/callers/illumina-strelka
@@ -41,6 +41,6 @@ rm -rf "$output_dir"/results "$output_dir"/workspace "$output_dir"/workflow* "$o
 --runDir "$output_dir" --config "$config" --exome \
 --indelCandidates "$illumina_dir"/results/variants/candidateSV.vcf.gz
 
-"$output_dir"/runWorkflow.py -j 24 && \
+"$output_dir"/runWorkflow.py -m local && \
 bgzip -d "$output_dir"/results/variants/genome.S1.vcf.gz && \
 ln -sf results/variants/genome.S1.vcf "$output_dir/illumina-strelka.vcf"