From 382be8c796a6ebe98640ca206af5c0017236f4b2 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 27 Mar 2019 21:17:13 -0500
Subject: [PATCH] Rename fastqs by sample not lane
---
workflow/main.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 3649ddf..7c37798 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -188,7 +188,7 @@ process count302 {
input:
- set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples302
+ set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz") from samples302
file ref from refLocation302.first()
expectCells302
forceCells302
@@ -217,4 +217,4 @@ process count302 {
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302 --chemistry="$chemistryParam302"
"""
}
-}
\ No newline at end of file
+}
--
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