From 4c9062b8a91bcda98716634377cfe5959ff399f3 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 20 Apr 2020 18:32:28 -0500
Subject: [PATCH] Add ulimit -u to all cellranger processes
---
workflow/main.nf | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/workflow/main.nf b/workflow/main.nf
index 1194038..586dd19 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -164,6 +164,7 @@ process count211 {
if (forceCells211 == 0) {
"""
hostname
+ ulimit -u 16384
ulimit -a
bash ${baseDir}/scripts/filename_check.sh -r ${ref}
cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells211} --chemistry=${chemistryParam211}
@@ -173,6 +174,7 @@ process count211 {
else {
"""
hostname
+ ulimit -u 16384
ulimit -a
bash ${baseDir}/scripts/filename_check.sh -r ${ref}
cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells211} --chemistry=${chemistryParam211}
@@ -208,6 +210,7 @@ process count220 {
if (forceCells220 == 0) {
"""
hostname
+ ulimit -u 16384
ulimit -a
bash ${baseDir}/scripts/filename_check.sh -r ${ref}
cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells220} --chemistry=${chemistryParam220}
@@ -217,6 +220,7 @@ process count220 {
else {
"""
hostname
+ ulimit -u 16384
ulimit -a
bash ${baseDir}/scripts/filename_check.sh -r ${ref}
cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --force-cells=${forceCells220} --chemistry=${chemistryParam220}
@@ -298,6 +302,7 @@ process count310 {
if (forceCells310 == 0) {
"""
hostname
+ ulimit -u 16384
ulimit -a
bash ${baseDir}/scripts/filename_check.sh -r ${ref}
cellranger count --id=${sample} --transcriptome=./${ref} --fastqs=. --sample=${sample} --expect-cells=${expectCells310} --chemistry=${chemistryParam310}
--
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