Update docs

CHANGELOG.md

@@ -7,6 +7,7 @@
 * Upload execution run
 * Upload mRNA QC
 * Create and upload output bag
+* Add optional to not upload
 
 **Background**
 * Remove (comment out) option to pull references from S3

README.md

@@ -34,9 +34,12 @@ To Run:
     * **dev** = [dev.gudmap.org](dev.gudmap.org) (default, does not contain all data)
     * **staging** = [staging.gudmap.org](staging.gudmap.org) (does not contain all data)
     * **production** = [www.gudmap.org](www.gudmap.org) (***does contain  all data***)
-  * `--refMoVersion` mouse reference version ***(optional)***
-  * `--refHuVersion` human reference version ***(optional)***
-  * `--refERCCVersion` human reference version ***(optional)***
+  * `--refMoVersion` mouse reference version ***(optional, default = 38.p6.vM22)***
+  * `--refHuVersion` human reference version ***(optional, default = 38.p12.v31)***
+  * `--refERCCVersion` human reference version ***(optional, default = 92)***
+  * `--upload` option to not upload output back to the data-hub ***(optional, default = true)***
+    * **true** = upload outputs to the data-hub
+    * **false** = do *NOT* upload outputs to the data-hub
   * `-profile` config profile to use ***(optional)***:
     * defaut = processes on BioHPC cluster
     * **biohpc** = process on BioHPC cluster