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.gitlab-ci.yml

@@ -1091,35 +1091,38 @@ aws:
     - export AWS_ACCESS_KEY_ID=${aws_accesskeyid}
     - export AWS_SECRET_ACCESS_KEY=${aws_secretaccesskey}
     - aws configure set region ${aws_region}
-    - aws s3 cp ./test_data/auth/ s3://bicf-output/ci-env/auth/ --exclude "*" --include "c*" --recursive
-    - aws s3 cp ./test_data/fastq/xsmall/ s3://bicf-output/ci-env/input/ --exclude "*" --include "Q-Y5F6_10K.R*.fastq.gz" --recursive
+    - aws s3 cp ./test_data/auth/ s3://bicf-nf-output/ci-env/auth/ --exclude "*" --include "c*" --recursive
+    - aws s3 cp ./test_data/fastq/xsmall/ s3://bicf-nf-output/ci-env/input/ --exclude "*" --include "Q-Y5F6_10K.R*.fastq.gz" --recursive
     - >
       id=$(aws batch submit-job\
         --job-name nf-GUDMAP_RBK_ci-env\
         --job-queue default-bicf\
-        --job-definition nextflow-bicf-nextflow\
+        --job-definition nextflow-nf\
         --container-overrides command=$(envsubst < ./docs/nxf_aws-ci-test.json))
       id=$(echo ${id}| grep -oP "jobId\K.*" | tr -d '"' | tr -d ":" | tr -d " " | tr -d "}")
     - >
       status=$(aws batch describe-jobs --jobs ${id} | grep -oP "status\": \K.*" | tr -d '"' | tr -d ',' | tr -d " " ) &&
       until [[ "${status}" == "SUCCEEDED" || "${status}" == "FAILED" ]]; do
         status=$(aws batch describe-jobs --jobs ${id} | grep -oP "status\": \K.*" | tr -d '"' | tr -d ',' | tr -d " " ) &&
-        echo ${status} &&
-        sleep 5m
+        echo ${status}
+        if [ "${status}" != "SUCCEEDED" ] && [ "${status}" != "FAILED" ]; then
+          sleep 1m
+        fi
       done
     - >
       if [ "${status}" == "SUCCEEDED" ]; then
         curl --request GET https://img.shields.io/badge/Envronment%3A%20AWS-run%20succesful-success?style=flat > ./badges/env/aws.svg
       else
         curl --request GET https://img.shields.io/badge/Envronment%3A%20AWS-run%20failed-critical?style=flat > ./badges/env/aws.svg
+        exit 1
       fi
   after_script:
     - module load awscli/1.11.139
     - 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
+    - aws s3 rm s3://bicf-nf-output/ci-env/auth/ --recursive
+    - aws s3 rm s3://bicf-nf-output/ci-env/input/ --recursive
   artifacts:
     when: always
     paths: