From 911127be17e847ca2c83027b157a95378fa6c821 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 20 Nov 2020 10:56:58 -0600
Subject: [PATCH] Change 5GEXSE to 5GEXR2
---
astrocyte_pkg.yml | 2 +-
workflow/main.nf | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index d1cc705..74f1ebf 100755
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -145,7 +145,7 @@ workflow_parameters:
- ['3GEXv2', '3prime GEX v2 (3prime Gene Expression)']
- ['5GEX', '5prime GEX Auto (5prime Gene Expression)']
- ['5GEXPE', '5prime GEX both R1 and R2 used for alignment (5prime Gene Expression)']
- - ['5GEXSE', '5prime GEX only R2 used for alignment (5prime Gene Expression)']
+ - ['5GEXR2', '5prime GEX only R2 used for alignment (5prime Gene Expression)']
required: true
description: |
10x single cell gene expression chemistry version (only used in cellranger version 3.x).
diff --git a/workflow/main.nf b/workflow/main.nf
index 5de18fb..e9f5afb 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -56,7 +56,7 @@ if (params.astrocyte) {
params.chemistryParam ='fiveprime'
} else if (params.kitVersion == "5GEXPE") {
params.chemistryParam ='SC5P-PE'
- } else if (params.kitVersion == "5GEXSE") {
+ } else if (params.kitVersion == "5GEXR2") {
params.chemistryParam ='SC5P-R2'
} else {
params.chemistryParam = 'auto'
--
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