increasing max heap memory allowed for the snpeff processes

nrminor · Nov 7, 2024 · 6c99adf · 6c99adf
1 parent dc2fd8d
commit 6c99adf
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git 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
@@ -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 \