Add 5prime chemistry option

astrocyte_pkg.yml

@@ -135,9 +135,10 @@ workflow_parameters:
     type: select
     default: 'auto'
     choices:
-      - ['auto', 'Auto Detect']
-      - ['three', '3']
-      - ['two', '2']
+      - ['auto', "Auto Detect"]
+      - ['3GEXv3', "3'GEX v3 (3' Gene Expression)"]
+      - ['3GEXv2', "3'GEX v2 (3' Gene Expression)"]
+      - ['5GEX', "5'GEX Auto (5' Gene Expression)"]
     required: true
     description: |
       10x single cell gene expression chemistry version (only used in cellranger version 3.x).

cleanup.sh

+rm *.out
+rm pipeline_trace*.txt*
+rm report*.html*
+rm timeline*.html*
+rm .nextflow*.log*
+rm -r .nextflow/
+rm -r work/

workflow/main.nf

@@ -31,12 +31,14 @@ if (params.kitVersion == "three" && params.version == '2.1.1') {
 if (params.astrocyte) {
   print("Running under astrocyte")
   params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
-  if (params.kitVersion == "one") {
+  if (params.kitVersion == "3GEXv1") {
     params.chemistryParam ='SC3Pv1'
-  } else if (params.kitVersion == "two") {
+  } else if (params.kitVersion == "3GEXv2") {
     params.chemistryParam ='SC3Pv2'
-  } else if (params.kitVersion == "three") {
+  } else if (params.kitVersion == "3GEXv3") {
     params.chemistryParam ='SC3Pv3'
+  } else if (params.kitVersion == "5GEX") {
+    params.chemistryParam ='fiveprime'
   } else {
     params.chemistryParam = 'auto'
   }
@@ -358,4 +360,4 @@ process multiqc {
     multiqc -c ${multiqcConf} .
     """
 
-}
+}
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