Update docs

CHANGELOG.md

@@ -2,6 +2,7 @@
 **User Facing**
 * Check Design File for spaces in name and file contents
 * Attempt to preven thredding error (which appears to only happen on 256GBv1 nodes)
+* Add option for 5' GEX chemistry
 
 **Background**
 * Add Nextflow Tower integration into CI (GHH's profile)

README.md

@@ -77,9 +77,10 @@ To Run:
     * --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
     * options:
         * *'auto'*
-        * *'three'*
-        * *'two'*
-    * eg: **--kitVersion 'three'**
+        * *'3GEXv3'*
+        * *'3GEXv2'*
+        * *'5GEX'*
+    * eg: **--kitVersion '3GEXv3'**
   * **--version**
     * cellranger version
     * --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
@@ -94,7 +95,7 @@ To Run:
     * eg: **--outDir 'test'**
 * FULL EXAMPLE:
   ```
-  nextflow run workflow/main.nf --fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/*.fastq.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/design.csv' --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.1.0' --outDir 'test'
+  nextflow run workflow/main.nf --fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/*.fastq.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/design.csv' --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0' --outDir 'test'
   ```
 * Design example: