diff --git a/README.md b/README.md
index c525c85c71bbcf7c81e2a2c32f05c3a05f923aa7..73b117596bc2a159d8c01398c5a0d1063cd96328 100644
--- a/README.md
+++ b/README.md
@@ -13,17 +13,37 @@ This pipeline was created to be a standard mRNA-sequencing analysis pipeline whi
 
 ![flowchart](docs/RNA-Seq%20Pipeline%20Design%20Flowchart.jpg "Flowchart")
 
+Cloud Compatibility:
+--------------------
+This pipeline is also capable of being run on AWS. To do so:
+* Build a AWS batch queue and environment either manually or with [aws-cloudformantion](https://console.aws.amazon.com/cloudformation/home?#/stacks/new?stackName=Nextflow&templateURL=https://s3.amazonaws.com/aws-genomics-workflows/templates/nextflow/nextflow-aio.template.yaml)
+* Edit one of the aws configs in workflow/config/
+  * Replace workDir with the S3 bucket generated
+  * Change region if different
+  * Change queue to the aws batch queue generated
+* The user must have awscli configured with an appropriate authentication (with ```aws configure``` and access keys) in the environment which nextflow will be run
+* Add ```-profile ``` with the name aws config which was customized
+
 To Run:
 -------
 * Available parameters:
-  * *--deriva* active ```credential.json``` file from [deriva-auth](https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Uploading-files-via-Deriva-client-tools#from-a-remote-server)
-  * *--bdbag* active ```cookies.txt``` file from [deriva-auth](https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Uploading-files-via-Deriva-client-tools#from-a-remote-server)
-  * *--repRID* mRNA-seq replicate RID\
-  note: once deriva-auth is run and authenticated, the two files above are saved in ```~/.deriva/``` (see official documents from [deriva](https://github.com/informatics-isi-edu/deriva-client#installer-packages-for-windows-and-macosx) on the lifetime of the credentials)
-* FULL EXAMPLE:
-  ```
-  nextflow run workflow/rna-seq.nf --deriva ./data/credential.json --bdbag ./data/cookies.txt --repRID Q-Y5JA
-  ```
+  * ```--deriva``` active **credential.json** file from [deriva-auth](https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Uploading-files-via-Deriva-client-tools#from-a-remote-server)
+  * ```--bdbag``` active **cookies.txt** file from [deriva-auth](https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Uploading-files-via-Deriva-client-tools#from-a-remote-server)
+  * ```--repRID``` mRNA-seq replicate RID
+  * ```--refMoVersion``` mouse reference version ***(optional)***
+  * ```--refHuVersion``` human reference version ***(optional)***
+  * ```-profile``` config profile to use: standard = local processes on BioHPC (default), biohpc = BioHPC cluster, aws_ondemand = AWS Batch on-demand instant requests, aws_spot = AWS Batch spot instance requests ***(optional)***
+* NOTES:
+  * once deriva-auth is run and authenticated, the two files above are saved in ```~/.deriva/``` (see official documents from [deriva](https://github.com/informatics-isi-edu/deriva-client#installer-packages-for-windows-and-macosx) on the lifetime of the credentials)
+  * reference version consists of Genome Reference Consortium version, patch release and GENCODE annotation release # (leaving the params blank will use the default version tied to the pipeline version)
+    * *current mouse* **38.p6.vM22** = GRCm38.p6 with GENCODE annotation release M22
+    * *current human* **38.p6.v31** = GRCh38.p12 with GENCODE annotation release 31
+
+FULL EXAMPLE:
+-------------
+```
+nextflow run workflow/rna-seq.nf --deriva ./data/credential.json --bdbag ./data/cookies.txt --repRID Q-Y5JA
+```
 
 
 
@@ -33,7 +53,7 @@ To Run:
 
 Credits
 =======
-This worklow is was developed by [Bioinformatic Core Facility (BICF), Department of Bioinformatics](http://www.utsouthwestern.edu/labs/bioinformatics/)
+This workflow is was developed by [Bioinformatic Core Facility (BICF), Department of Bioinformatics](http://www.utsouthwestern.edu/labs/bioinformatics/)
 
 PI
 --