diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5dc43603a40dd59ce926bf9a69f2655b7069f99e..a09f1786745c1678022cc9c8516b6bb7c61d1cea 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1054,3 +1054,72 @@ dnanexus:
     paths:
       - badges/
   allow_failure: true
+
+  aws:
+    stage: environment
+    only:
+      variables:
+        - $awsEnv == "true"
+    except:
+      - push
+      - tags
+      - merge_requests
+    script:
+      - hostname
+      - ulimit -a
+      - mkdir -p ./badges/env
+      - curl --request GET https://img.shields.io/badge/Envronment%3A%20AWS-inactive-critical?style=flat > ./badges/env/aws.svg
+      - module load awscli/1.19.17
+      - >
+        export AWS_ACCESS_KEY_ID=${aws_accesskeyid}
+        export AWS_SECRET_ACCESS_KEY=${aws_secretaccesskey}
+        aws configure set region ${aws_region}
+      - aws s3 cp ./test_data/auth/ s3://bicf-output/ci-env/auth/ --exclude "*" --include "c*" --recursive
+      - aws s3 cp ./test_data/fastq/xsmall/ s3://bicf-output/ci-env/input/ --exclude "*" --include "Q-Y5F6_10K.R*.fastq.gz" --recursive
+      - >
+        id=$(aws batch submit-job\
+          --job-name nf-GUDMAP_RBK_ci-env\
+          --job-queue default-bicf\
+          --job-definition nextflow-bicf-nextflow\
+          --container-overrides command=\
+            "utsw-bicf/gudmap_rbk.rna-seq","-r","env.ci",\
+            "-profile","aws",\
+            "--deriva","s3://bicf-output/ci-env/auth/credential.json",\
+            "--bdbag","s3://bicf-output/ci-env/auth/cookies.txt",\
+            "--repRID","Q-Y5F6",\
+            "--source","staging",\
+            "--upload","false",\
+            "--dev","false",\
+            "--ci","true",\
+            "--track","false",\
+            "-with-report","s3://bicf-output/ci-env/output/Q-Y5F6_fastqoverride_report.html",\
+            "--refSource","datahub",\
+            "--outDir","s3://bicf-output/ci-env/output/Q-Y5F6_fastqoverride",\
+            "--fastqsForce","s3://bicf-output/ci-env/input/*.fastq.gz")
+        id=$(echo ${id}| grep -oP "jobId\K.*" | tr -d '"' | tr -d ":" | tr -d " " | tr -d "}")
+      - >
+        status=$(aws batch describe-jobs --jobs ${id} | grep -oP "status\": \K.*" | tr -d '"' | tr -d ',') &&
+        until [[ "${status}" == "SUCCEEDED" || "${status}" == "FAILED" ]]; do
+          status=$(aws batch describe-jobs --jobs ${id} | grep -oP "status\": \K.*" | tr -d '"' | tr -d ',') &&
+          echo ${status} &&
+          sleep 30
+        done
+      - >
+        if [ "${status}" == "SUCCEEDED" ]; then
+          curl --request GET https://img.shields.io/badge/Envronment%3A%20AWS-run%20succesful-success?style=flat > ./badges/env/dnanexus.svg
+        else
+          curl --request GET https://img.shields.io/badge/Envronment%3A%20AWS-run%20failed-critical?style=flat > ./badges/env/dnanexus.svg
+        fi
+    after_script:
+      - module load awscli/1.19.17
+      - >
+        export AWS_ACCESS_KEY_ID=${aws_accesskeyid}
+        export AWS_SECRET_ACCESS_KEY=${aws_secretaccesskey}
+        aws configure set region ${aws_region}
+      - aws s3 rm s3://bicf-output/ci-env/auth/ --recursive
+      - aws s3 rm s3://bicf-output/ci-env/input/ --recursive
+    artifacts:
+      when: always
+      paths:
+        - badges/
+    allow_failure: true
\ No newline at end of file