From 4ab098733a8f7df71e6b83af2893f3e6aa3a7bfc Mon Sep 17 00:00:00 2001
From: Benjamin Wingfield <bwingfield@ebi.ac.uk>
Date: Tue, 1 Mar 2022 18:13:05 +0000
Subject: [PATCH] set memory in MB (#1260)

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
---
 modules/plink2/extract/main.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/plink2/extract/main.nf b/modules/plink2/extract/main.nf
index 89cffdc3..15f9c038 100644
--- a/modules/plink2/extract/main.nf
+++ b/modules/plink2/extract/main.nf
@@ -23,11 +23,13 @@ process PLINK2_EXTRACT {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     if( "$pgen" == "${prefix}.pgen" ) error "Input and output names are the same, use \"task.ext.prefix\" in modules.config to disambiguate!"
+    def mem_mb = task.memory.toMega()
     """
     plink2 \\
+        --threads $task.cpus \\
+        --memory $mem_mb \\
         --pfile ${pgen.baseName} \\
         $args \\
-        --threads $task.cpus \\
         --extract $variants \\
         --make-pgen vzs \\
         --out ${prefix}