Add back use params in config

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