From 79e40633b7cb40c50159843e5d0117016a99f133 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 20 Nov 2020 10:25:18 -0600
Subject: [PATCH] Add all library options to main.nf
---
workflow/main.nf | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 532b661..5de18fb 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -44,7 +44,9 @@ if (params.astrocyte) {
} else {
params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
}
- if (params.kitVersion == "3GEXv1") {
+ if (params.kitVersion == "3GEX") {
+ params.chemistryParam ='threeprime'
+ } else if (params.kitVersion == "3GEXv1") {
params.chemistryParam ='SC3Pv1'
} else if (params.kitVersion == "3GEXv2") {
params.chemistryParam ='SC3Pv2'
@@ -52,6 +54,10 @@ if (params.astrocyte) {
params.chemistryParam ='SC3Pv3'
} else if (params.kitVersion == "5GEX") {
params.chemistryParam ='fiveprime'
+ } else if (params.kitVersion == "5GEXPE") {
+ params.chemistryParam ='SC5P-PE'
+ } else if (params.kitVersion == "5GEXSE") {
+ params.chemistryParam ='SC5P-R2'
} else {
params.chemistryParam = 'auto'
}
--
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