From a2733bff87b84ac5480239d46328b0311ebb7927 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 11 Sep 2018 11:33:10 -0500
Subject: [PATCH] Embed module load cellranger into if/then/else
---
workflow/main.nf | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 294f3fa..7fef409 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -71,15 +71,14 @@ process count {
file("**/outs/**") into outPaths
script:
- """
- module load cellranger/2.1.1
- """
if (forceCells == 0){
"""
+ module load cellranger/2.1.1
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells
"""
} else {
"""
+ module load cellranger/2.1.1
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells
"""
}
--
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