From 6c99adf9d99afdf5f3ea11df953bf549cec9dd51 Mon Sep 17 00:00:00 2001
From: Nicholas Minor <nrminor@wisc.edu>
Date: Thu, 7 Nov 2024 16:30:42 -0600
Subject: [PATCH] increasing max heap memory allowed for the snpeff processes

---
 lib/Utils.groovy  | 2 +-
 modules/snpeff.nf | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/Utils.groovy b/lib/Utils.groovy
index 895f775..3acd2fd 100644
--- a/lib/Utils.groovy
+++ b/lib/Utils.groovy
@@ -140,7 +140,7 @@ class Utils {
                 Illumina FASTQs directory   : ${params.illumina_fastq_dir ?: ""}
                 Sample ID lookup            : ${params.sample_lookup ?: ""}
                 Results directory           : ${params.results}
-                Email Address(es)            : ${params.email ?: ""}
+                Email Address(es)           : ${params.email ?: ""}
 
                 """
                 .stripIndent()
diff --git a/modules/snpeff.nf b/modules/snpeff.nf
index e615e43..0199121 100644
--- a/modules/snpeff.nf
+++ b/modules/snpeff.nf
@@ -50,7 +50,7 @@ process ANNOTATE_VCF {
     script:
     """
     cp ${snpeff_config} local.config && \
-    snpEff -Xmx1g \
+    snpEff -Xmx3g \
     -c local.config \
     -dataDir genome/ \
     -v ref_genome \
@@ -77,7 +77,7 @@ process EXTRACT_FIELDS {
 
     script:
     """
-    SnpSift -Xmx1g extractFields \
+    SnpSift -Xmx3g 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 \