Set options reguardless of astrocyte

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