From c47179850011bff5031c90513877aa9e31b223ea Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 13 Apr 2020 21:43:49 -0500
Subject: [PATCH] Add back use params in config
---
workflow/main.nf | 27 +++++++++++++++++----------
1 file changed, 17 insertions(+), 10 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index d839b94..a9a6f32 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -28,18 +28,25 @@ if (params.kitVersion == "3GEXv3" && params.version == '2.1.1') {
System.exit(32)
}
-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'
+// Assign variables if astrocyte
+if (params.astrocyte) {
+ print("Running under astrocyte")
+ params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
+ if (params.kitVersion == "one") {
+ params.chemistryParam ='SC3Pv1'
+ } else if (params.kitVersion == "two") {
+ params.chemistryParam ='SC3Pv2'
+ } else if (params.kitVersion == "three") {
+ params.chemistryParam ='SC3Pv3'
+ } else {
+ params.chemistryParam = 'auto'
+ }
} else {
- params.chemistryParam = 'auto'
+ 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.genomeLocationFull = params.genomeLocation+params.genome
// Define regular variables
--
GitLab