From ab2a960fc0252ee5193c5d831ca91f99a5a27e16 Mon Sep 17 00:00:00 2001
From: mflynn <mflynn@lanl.gov>
Date: Mon, 29 Jul 2024 15:13:25 -0600
Subject: [PATCH] set memory usage in runtime and added set -euo pipefail in
 command

---
 data/workflow/WDL/metaT/metat_assembly.wdl | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/data/workflow/WDL/metaT/metat_assembly.wdl b/data/workflow/WDL/metaT/metat_assembly.wdl
index 8ae654a2..d8465e6d 100755
--- a/data/workflow/WDL/metaT/metat_assembly.wdl
+++ b/data/workflow/WDL/metaT/metat_assembly.wdl
@@ -8,6 +8,7 @@ task megahit_assembly{
 
 #  parameter from https://www.nature.com/articles/s41597-019-0132-4
 	command <<<
+	    set -euo pipefail
 		megahit --12 ${rqc_clean_reads[0]}  -t ${no_of_cpus} -o out/ --out-prefix mh --k-list 23,43,63,83,103,123
         mkdir -p ${assem_out_fdr}
 		cat out/mh.contigs.fa |sed 's/>.*_/>${assem_out_prefix}_/'|sed 's/ .*//' > ${assem_out_fdr}/${assem_out_prefix}.contigs.fa
@@ -20,6 +21,7 @@ task megahit_assembly{
 	runtime {
 		docker: DOCKER
 		cpu: no_of_cpus
+		memory: "120 GiB"
 	}
 
 	output{