From 2fb6128644c4c5c92105a0c2659b25a01d4509cb Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 11 Sep 2018 10:16:45 -0500
Subject: [PATCH] Point transcriptome to ./
---
workflow/main.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index e248a15..294f3fa 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -76,11 +76,11 @@ process count {
"""
if (forceCells == 0){
"""
- cellranger count --id="$sample" --transcriptome="$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells
+ cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells
"""
} else {
"""
- cellranger count --id="$sample" --transcriptome="$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells
+ cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells
"""
}
}
--
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