From cf9d3be891c2fb083de882436639afab1e93c655 Mon Sep 17 00:00:00 2001
From: David Trudgian <David.Trudgian@UTSouthwestern.edu>
Date: Thu, 21 Mar 2019 16:20:36 -0500
Subject: [PATCH] Fix astrocyte param for implicit boolean conversion
---
workflow/main.nf | 16 +++++++++-------
1 file changed, 9 insertions(+), 7 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 7ed5bca..bb2946d 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -14,16 +14,12 @@ params.forceCells = 0
params.kitVersion = 'three'
params.version = '3.0.2'
-params.astrocyte = 'false'
+params.astrocyte = false
params.outDir = "$baseDir/output"
// Assign variables if astrocyte
-if (params.astrocyte == 'false') {
- 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
-} else if (params.astrocyte == 'true') {
+if (params.astrocyte) {
+ print("Running under astrocyte")
params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
if (params.kitVersion == "one") {
params.chemistryParam ='SC3Pv1'
@@ -34,6 +30,12 @@ if (params.astrocyte == 'false') {
} else {
params.chemistryParam = 'auto'
}
+} 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.genomeLocationFull = params.genomeLocation+params.genome
--
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