From 8694f2163aab7617e409eb6cecb4a2562dd01079 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Wed, 28 Jul 2021 09:17:48 +0100
Subject: [PATCH] Update main.nf

---
 main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/main.nf b/main.nf
index fa9c455ac..25d4e498a 100755
--- a/main.nf
+++ b/main.nf
@@ -1030,9 +1030,9 @@ process PHANTOMPEAKQUALTOOLS {
     script:
     """
     RUN_SPP=`which run_spp.R`
-    Rscript -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="${bam[0]}" -savp="${name}.spp.pdf" -savd="${name}.spp.Rdata" -out="${name}.spp.out" -p=$task.cpus
+    Rscript --max-ppsize=500000 -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="${bam[0]}" -savp="${name}.spp.pdf" -savd="${name}.spp.Rdata" -out="${name}.spp.out" -p=$task.cpus
     cp $spp_correlation_header ${name}_spp_correlation_mqc.tsv
-    Rscript -e "load('${name}.spp.Rdata'); write.table(crosscorr\\\$cross.correlation, file=\\"${name}_spp_correlation_mqc.tsv\\", sep=",", quote=FALSE, row.names=FALSE, col.names=FALSE,append=TRUE)"
+    Rscript --max-ppsize=500000 -e "load('${name}.spp.Rdata'); write.table(crosscorr\\\$cross.correlation, file=\\"${name}_spp_correlation_mqc.tsv\\", sep=",", quote=FALSE, row.names=FALSE, col.names=FALSE,append=TRUE)"
 
     awk -v OFS='\t' '{print "${name}", \$9}' ${name}.spp.out | cat $spp_nsc_header - > ${name}_spp_nsc_mqc.tsv
     awk -v OFS='\t' '{print "${name}", \$10}' ${name}.spp.out | cat $spp_rsc_header - > ${name}_spp_rsc_mqc.tsv