From 66e8e13f379f4c28bd97c34d934aad8606c3cde5 Mon Sep 17 00:00:00 2001
From: samarth8392 <samarth.mathur@nih.gov>
Date: Thu, 26 Sep 2024 12:28:32 -0400
Subject: [PATCH] fix: use appropriate java jdk.

---
 workflow/rules/qc.smk                  | 2 +-
 workflow/rules/somatic_snps.common.smk | 2 +-
 workflow/rules/somatic_snps.paired.smk | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk
index b5f1eaa..1e45b6c 100644
--- a/workflow/rules/qc.smk
+++ b/workflow/rules/qc.smk
@@ -390,7 +390,7 @@ rule snpeff:
     envmodules: config['tools']['snpEff']['modname']
     container: config['images']['wes_base']
     shell: """
-    java -Xmx12g -jar $SNPEFF_JAR \\
+    java8 -Xmx12g -jar $SNPEFF_JAR \\
         -v -canon -c {params.config} \\
         -csvstats {output.csv} \\
         -stats {output.html} \\
diff --git a/workflow/rules/somatic_snps.common.smk b/workflow/rules/somatic_snps.common.smk
index 27e6989..121b2c7 100644
--- a/workflow/rules/somatic_snps.common.smk
+++ b/workflow/rules/somatic_snps.common.smk
@@ -168,7 +168,7 @@ rule somatic_merge_callers:
       mkdir -p "$(dirname {output.mergedvcf})"
     fi
 
-    java -Xmx60g -Djava.io.tmpdir=${{tmp}} -jar $GATK_JAR -T CombineVariants \\
+    java8 -Xmx60g -Djava.io.tmpdir=${{tmp}} -jar $GATK_JAR -T CombineVariants \\
         -R {params.genome} \\
         -nt {threads} \\
         --filteredrecordsmergetype KEEP_IF_ANY_UNFILTERED \\
diff --git a/workflow/rules/somatic_snps.paired.smk b/workflow/rules/somatic_snps.paired.smk
index 1f5427b..42e902e 100644
--- a/workflow/rules/somatic_snps.paired.smk
+++ b/workflow/rules/somatic_snps.paired.smk
@@ -147,7 +147,7 @@ rule strelka:
     cd "$myoutdir"
     ./runWorkflow.py -m local -j {threads}
 
-    java -Xmx12g -Djava.io.tmpdir=${{tmp}} -XX:ParallelGCThreads={threads} \\
+    java8 -Xmx12g -Djava.io.tmpdir=${{tmp}} -XX:ParallelGCThreads={threads} \\
         -jar $GATK_JAR -T CombineVariants \\
         -R {params.genome} \\
         --variant results/variants/somatic.snvs.vcf.gz \\
@@ -439,7 +439,7 @@ rule varscan_paired:
     awk '{{gsub(/\y[W|K|Y|R|S|M|B|D|H|V]\y/,"N",$4); OFS = "\t"; print}}' {output.vcf}.indel \\
         | sed '/^$/d' > {output.vcf}.indel_temp
 
-    java -Xmx12g -Djava.io.tmpdir=${{tmp}} -XX:ParallelGCThreads={threads} \\
+    java8 -Xmx12g -Djava.io.tmpdir=${{tmp}} -XX:ParallelGCThreads={threads} \\
         -jar $GATK_JAR -T CombineVariants \\
         -R {params.genome} \\
         --variant {output.vcf}.snp_temp \\