From a1edc5821ccd44a70585e5711a4cfeb60951178a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 13 Apr 2020 11:17:21 -0500
Subject: [PATCH] Set options reguardless of astrocyte
---
workflow/main.nf | 30 +++++++++++-------------------
1 file changed, 11 insertions(+), 19 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 92c5569..e6fa478 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -13,6 +13,7 @@ params.name = "run"
params.fastq = "${baseDir}/../test_data/*.fastq.gz"
params.designFile = "${baseDir}/../test_data/design.csv"
params.genome = 'GRCh38-3.0.0'
+params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
params.expectCells = 10000
params.forceCells = 0
params.kitVersion = '3GEXv3'
@@ -27,27 +28,18 @@ if (params.kitVersion == "3GEXv3" && params.version == '2.1.1') {
System.exit(32)
}
-// Assign variables if astrocyte
-if (params.astrocyte) {
- print("Running under astrocyte")
- params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
- if (params.kitVersion == "3GEXv1") {
- params.chemistryParam ='SC3Pv1'
- } else if (params.kitVersion == "3GEXv2") {
- params.chemistryParam ='SC3Pv2'
- } else if (params.kitVersion == "3GEXv3") {
- params.chemistryParam ='SC3Pv3'
- } else if (params.kitVersion == "5GEX") {
- params.chemistryParam ='fiveprime'
- } else {
- params.chemistryParam = 'auto'
- }
+if (params.kitVersion == "3GEXv1") {
+ params.chemistryParam ='SC3Pv1'
+} else if (params.kitVersion == "3GEXv2") {
+ params.chemistryParam ='SC3Pv2'
+} else if (params.kitVersion == "3GEXv3") {
+ params.chemistryParam ='SC3Pv3'
+} else if (params.kitVersion == "5GEX") {
+ params.chemistryParam ='fiveprime'
} else {
- params.genomes = []
- params.genomeLocation = params.genome ? params.genomes[ params.genome ].loc ?: false : false
- params.chemistry = []
- params.chemistryParam = params.kitVersion ? params.chemistry[ params.kitVersion ].param ?: false : false
+ params.chemistryParam = 'auto'
}
+
params.genomeLocationFull = params.genomeLocation+params.genome
// Define regular variables
--
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