From 260389ed333c6dd19c0cc9fe1f7b9922cff5de82 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 29 Apr 2021 12:24:47 +0200
Subject: [PATCH] kb: add -m option to control memory
---
src/nf_modules/kb/main.nf | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/kb/main.nf b/src/nf_modules/kb/main.nf
index 97d90b27..fe08a0df 100644
--- a/src/nf_modules/kb/main.nf
+++ b/src/nf_modules/kb/main.nf
@@ -185,6 +185,7 @@ process kb_marseq {
tuple val(file_id), path("*_report.txt"), emit: report
script:
+ memory = "${task.memory}" - ~/\s*GB/
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
@@ -199,7 +200,7 @@ process kb_marseq {
"""
mkdir ${file_prefix}
kb count -t ${task.cpus} \
- -m ${task.memory} \
+ -m ${memory} \
-i ${index} \
-g ${transcript_to_gene} \
${whitelist_param} \
--
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