diff --git a/CHANGELOG.md b/CHANGELOG.md
index fe06f42c257925ff8110291afd8112117f7a6d56..97e74118d13b366d50c864570c4f319ff92701a9 100644
--- a/CHANGELOG.md
+++ b/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
diff --git a/README.md b/README.md
index 4baf67a6ce4626a309c5346fea705b51c722a3d4..c7002c709b2ab5b2781f8e1bc5f33cc8c1178b55 100644
--- a/README.md
+++ b/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