Merge branch '56-5GEX' into 'develop'

Resolve "Add 5GEXPE/SE as library options"

Closes #56

See merge request !80

CHANGELOG.md

 # v3.0.0
 **User Facing**
-* 
+* Add 5GEX-PE, 5GEX-R2, threeprime as library options
 
 **Background**
 
 *Known Bugs*
 * Vizapp does not yet work for Astrocyte
 * Running in CLI: to set --fastq path of file/s needs to be in quotes
+* 2020-A references don't work with with cellranger versions < 4.0.0 (bug)
 
 # v2.2.0
 **User Facing**

README.md

@@ -96,9 +96,12 @@ To Run:
     * --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
     * options:
         * *'auto'*
+        * *'3GEX'*
         * *'3GEXv3'*
         * *'3GEXv2'*
         * *'5GEX'*
+        * *'5GEXPE'*
+        * *'5GEXR2'*
     * eg: **--kitVersion '3GEXv3'**
   * **--version**
     * cellranger version

astrocyte_pkg.yml

@@ -140,9 +140,12 @@ workflow_parameters:
     default: 'auto'
     choices:
       - ['auto', 'Auto Detect']
+      - ['3GEX', '3prime GEX Auto (3prime Gene Expression)']
       - ['3GEXv3', '3prime GEX v3 (3prime Gene Expression)']
       - ['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)']
+      - ['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

@@ -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 == "5GEXR2") {
+    params.chemistryParam ='SC5P-R2'
   } else {
     params.chemistryParam = 'auto'
   }