From c43d49d746e3322835adf7cbc320d8f042f5344c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 21 Mar 2019 15:01:07 -0500
Subject: [PATCH] Add hostname and ulimit -a to all processes for diagnosis
---
workflow/main.nf | 14 ++++++++++++++
1 file changed, 14 insertions(+)
diff --git a/workflow/main.nf b/workflow/main.nf
index c12e30d..ec068ca 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -71,6 +71,8 @@ process checkDesignFile {
script:
"""
+ hostname
+ ulimit -a
module load python/3.6.1-2-anaconda
python3 $baseDir/scripts/check_design.py -d $designLocation -f $fastqList
"""
@@ -129,10 +131,14 @@ process count211 {
"""
if (forceCells211 == 0){
"""
+ hostname
+ ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells211
"""
} else {
"""
+ hostname
+ ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells211
"""
}
@@ -165,10 +171,14 @@ process count301 {
"""
if (forceCells301 == 0){
"""
+ hostname
+ ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells301 --chemistry="$chemistryParam301"
"""
} else {
"""
+ hostname
+ ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells301 --chemistry="$chemistryParam301"
"""
}
@@ -201,10 +211,14 @@ process count302 {
"""
if (forceCells302 == 0){
"""
+ hostname
+ ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells302 --chemistry="$chemistryParam302"
"""
} else {
"""
+ hostname
+ ulimit -a
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302 --chemistry="$chemistryParam302"
"""
}
--
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