From b965b5d444f751dfd6b2c190221741886f77b0d7 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 12 Mar 2019 11:38:28 -0500
Subject: [PATCH] Add module loads to processes in main.nf until custom configs
fixed in astrocyte
---
workflow/main.nf | 10 ++++++++++
1 file changed, 10 insertions(+)
diff --git a/workflow/main.nf b/workflow/main.nf
index 90165b2..7ed5bca 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -71,6 +71,7 @@ process checkDesignFile {
script:
"""
+ module load python/3.6.1-2-anaconda
python3 $baseDir/scripts/check_design.py -d $designLocation -f $fastqList
"""
}
@@ -123,6 +124,9 @@ process count211 {
version == '2.1.1'
script:
+ """
+ module load cellranger/2.1.1
+ """
if (forceCells211 == 0){
"""
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells211
@@ -156,6 +160,9 @@ process count301 {
version == '3.0.1'
script:
+ """
+ module load cellranger/3.0.1
+ """
if (forceCells301 == 0){
"""
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells301 --chemistry="$chemistryParam301"
@@ -189,6 +196,9 @@ process count302 {
version == '3.0.2'
script:
+ """
+ module load cellranger/3.0.2
+ """
if (forceCells302 == 0){
"""
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells302 --chemistry="$chemistryParam302"
--
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