From dc2fd8d742ad3227690a0abfde574a2282f265e4 Mon Sep 17 00:00:00 2001
From: Nicholas Minor <nrminor@wisc.edu>
Date: Thu, 7 Nov 2024 16:02:09 -0600
Subject: [PATCH] introducing max heap memory limits for the snpeff/snpsift
 processes

---
 modules/snpeff.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/snpeff.nf b/modules/snpeff.nf
index 7defc5d..e615e43 100644
--- a/modules/snpeff.nf
+++ b/modules/snpeff.nf
@@ -50,7 +50,7 @@ process ANNOTATE_VCF {
     script:
     """
     cp ${snpeff_config} local.config && \
-    snpEff \
+    snpEff -Xmx1g \
     -c local.config \
     -dataDir genome/ \
     -v ref_genome \
@@ -77,7 +77,7 @@ process EXTRACT_FIELDS {
 
     script:
     """
-    SnpSift extractFields \
+    SnpSift -Xmx1g extractFields \
     -s "," \
     ${vcf} \
     CHROM REF POS ALT AF AC DP GEN[0].REF_DP GEN[0].ALT_DP GEN[0].ALT_FREQ MQ ANN[0].GENE ANN[0].EFFECT ANN[0].HGVS_P ANN[0].CDS_POS ANN[0].AA_POS \