Add all library options to main.nf

workflow/main.nf

@@ -44,7 +44,9 @@ if (params.astrocyte) {
   } else {
     params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
   }
-  if (params.kitVersion == "3GEXv1") {
+  if (params.kitVersion == "3GEX") {
+    params.chemistryParam ='threeprime'
+  } else if (params.kitVersion == "3GEXv1") {
     params.chemistryParam ='SC3Pv1'
   } else if (params.kitVersion == "3GEXv2") {
     params.chemistryParam ='SC3Pv2'
@@ -52,6 +54,10 @@ if (params.astrocyte) {
     params.chemistryParam ='SC3Pv3'
   } else if (params.kitVersion == "5GEX") {
     params.chemistryParam ='fiveprime'
+  } else if (params.kitVersion == "5GEXPE") {
+    params.chemistryParam ='SC5P-PE'
+  } else if (params.kitVersion == "5GEXSE") {
+    params.chemistryParam ='SC5P-R2'
   } else {
     params.chemistryParam = 'auto'
   }