Change 5GEXSE to 5GEXR2

astrocyte_pkg.yml

@@ -145,7 +145,7 @@ workflow_parameters:
       - ['3GEXv2', '3prime GEX v2 (3prime Gene Expression)']
       - ['5GEX', '5prime GEX Auto (5prime Gene Expression)']
       - ['5GEXPE', '5prime GEX both R1 and R2 used for alignment (5prime Gene Expression)']
-      - ['5GEXSE', '5prime GEX only R2 used for alignment (5prime Gene Expression)']
+      - ['5GEXR2', '5prime GEX only R2 used for alignment (5prime Gene Expression)']
     required: true
     description: |
       10x single cell gene expression chemistry version (only used in cellranger version 3.x).

workflow/main.nf

@@ -56,7 +56,7 @@ if (params.astrocyte) {
     params.chemistryParam ='fiveprime'
   } else if (params.kitVersion == "5GEXPE") {
     params.chemistryParam ='SC5P-PE'
-  } else if (params.kitVersion == "5GEXSE") {
+  } else if (params.kitVersion == "5GEXR2") {
     params.chemistryParam ='SC5P-R2'
   } else {
     params.chemistryParam = 'auto'