From f57ad93b7875cbeef8fa3d9928900f2600f2abe2 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 21 Feb 2020 10:46:18 -0600
Subject: [PATCH] Add ulimit -u to prevent thread error
---
workflow/main.nf | 3 +++
1 file changed, 3 insertions(+)
diff --git a/workflow/main.nf b/workflow/main.nf
index acd7d53..f5cdf75 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -242,6 +242,7 @@ process count302 {
if (forceCells302 == 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=${expectCells302} --chemistry=${chemistryParam302}
@@ -251,6 +252,7 @@ process count302 {
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=${forceCells302} --chemistry=${chemistryParam302}
@@ -295,6 +297,7 @@ process count310 {
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=${forceCells310} --chemistry=${chemistryParam310}
--
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